I finished up asking everybody in the Umpani Base Camp about everything: Panrack, Saxx, Bildublu, Kunar, Sparkle, Balbrak, and the EWAXX computer. All done with that area.
I then made my way through the Mount Gigas Caves, into the Upper Mount Gigas Caves, where I completely cleared the map. I even did the teleporter to the Umpani House, grabbing a 2nd Dulcimer of Mending (Heal All instrument, why are there 2)? It's just like with the Silent Lyre (Silence instrument, it's not like most parties will have 2 Bards).
My Gadgeteer now has 126 skill in Locks and Traps, if a PL7 Divine Trap spell is cast on a chest (strange that a skill can be above 125, this must be the only case).
I talked to both Yamir and Rubble about everything possible. Yamir gave orders to search Bayjin for any survivors of an exploration team, and Rubble is giving me on-the-job-training (basically, suit up in Scuba Gear, and make it happen).
I will do the Mount Gigas Water Caves tomorrow, it's really kind of a pointless map, nothing special. Just get from one end to the other, while dealing with annoying underwater enemies, and one miscellaneous slot taken up by Scuba Gear, and no Fire magic.
Edit: I also configured my portals, in preparation for rescuing Glumph, and the Alliance Quest later. One portal at the TRangaPorter (4 in 1), one at Z'Ant, one at Yamir, and one near the entrance to Mount Gigas Peak (where you need a Top Security Pass to enter).
In this way, Glumph, Drazic, and Rodan can all be instantly teleported to their leaders with no battles, and they can shoot down the Savant's Black Ship with no battles either.

My theory is that the developers considered the ability of a Bard to stamina cast Heal All to be vital enough that they wanted to ensure that you'd be able to get it regardless of whether you side with the Umpani or the T'Rang.

Then again, it's also rather curious that the item exists. There's an unused item from Wizardry 7, the Lyre of Cakes, that also casts this spell. (In Wizardry 7, it's possible to get this item, and it supposedly casts Healthful (the predecessor to Heal All, but it only heals half what Heal Wounds does, making the spell way too weak given how weak Heal Wounds is by the time you get that spell), though reports indicate it doesn't work properly. Unfortunately, this item does not import to Wizardry 8, and it's not placed in the game, so it goes unused. Interestingly enough, it exists in Wizardry 6 (unobtainable), and supposedly casts Helpfood, which is the spell that became Restore Health; that would have been interesting to be able to stamina cast.)

For the Silent Lyre, my guess is that they forgot about the first one when they added the second, or there could have been a communication issue between different level designers, causing each one to place the item in the level. Or, maybe a playtester didn't find the item, and therefore reported it not appearing as a bug (when its appearance was specified in some internal document), so they added a second one, not realizing that the first one was present and accessible.

I finished the Umpani quest-line, just like I did with the T'Rang. Both want me to destroy the other faction's Mothership (which I won't do for either).
The Mt. Gigas Water Caves map was cleared by doing the NE leg first (following the map perimeter), then the SW leg doubling back to the entrance, then the middle "loops" were checked out until I completely cleared the map of all set enemies, and all items, both hidden and obvious.
I returned to the North side of the Bayjin Shallows, near where I killed Nessie. It appears that she killed all of Glumph's platoon, as there are a few military IUF tags near skeletons. I then returned to Bayjin, above water, with little problem.
I made sure to explore the underwater parts of North Bayjin, as I want to be completely rid of Scuba Gear. The Sea Caves, Mt. Gigas Water Caves, Bayjin Shallows, and North Bayjin submerged areas were completely explored, let me assure you. I want to completely dump all of the Scuba Gear, and get back my second miscellaneous item slot.
Anyways, after a bunch of annoying, quickly-respawning battles in North Bayjin, I cleared out not only the water areas, but any enemies around the tents. I then entered the big tent, where Glumph was being held, and talked to him about everything. He was extremely disrespectful, and only answered one question, when asked about Bayjin, "get me far away from here!"
I portaled him quickly to Yamir, where he backed down from a confrontation (coward, all bark and no bite). I made sure to un-equip all the Scuba Gear, then re-equip all the good second miscellaneous equipment. Also, I gave Yamir the military tags of Glumph's team.
I made sure to do a triple-hard save, because this is the beginning of the Alliance Quest!

Does doing this do anything interesting?

Unfortunately, handing Yamir the IUF tags does nothing but a short, sad response. I talked to Glumph for the last time, and he actually thanked me for the rescue (he disappears forever after this). Yamir wants me to destroy the T'Rang Mothership at this point, so the Umpani questline is over.
Talking to all other Umpani members after rescuing Glumph has gotten me no responses at the Umpani Base Camp. Talking to Yamir again results in nothing, Glumph has disappeared forever, and Rubble is hanging out at the UTU training area forever. At least he acknowledges my hard work in rescuing Glumph, congratulating me for saving him, and mourning the loss of his platoon.

Anyways, onto the Umpani-T'Rang Alliance Quest! I had to slaughter so many Rapax, I lost count. I raided a couple of tents with 1 chest each, then the Rapax Prince talked $h!t to me, and teleported away, so I could kill his Concubines, and raid a couple of chests in that tent.
I had to kill a couple of Rapax Archers in a tower in the middle of the map, then I hit a strange device that seemed to disable communication between the remaining Rapax. Halfway through the map, I killed another group of 2 Rapax Archers, while neutral Templar Rapax stood by and did nothing.
I killed 2 Rapax Templars standing there by surprise, then mounted the last guard tower, killing 2 more by surprise. This alerted the last 8 Rapax Templars, and I killed all of them from the high point on the last tower. One of them, the Stockade Guard, dropped the Stockade Key, used to free Rodan and Drazic.
This left only the Rapax King and a nearby Templar Knight. Believe it or not, the Rapax King is immune to all instant death spells, so the battle went like this: I paralyzed both the King and his sidekick, instant killed the Templar Knight, then hacked the Rapax King to bits with the Bard's *Light Sword*, while he was still paralyzed. He dropped a key to free his wife, and I raided 3 treasure chests in his tent.
The Rapax Queen seems to be "on the level", opposing the Dark Savant-Rapax Alliance, and that's why she was locked up. She seems to be one of the rational Rapax, which is why I went through the effort to kill her husband and free her. Why won't she join my party, or just leave? I could recruit her, and portal her to Arnika, where she could meet up with Antone, and start a whole new life together. I guess that she would rather sit there, and contemplate the meaning of life.

I heard that there's an unfinished quest like that's supposed to involve her.

There's also the Rapax Assassins faction. I believe that faction has no members, but there is an action that will reduce your rating with that faction.

I managed to form an alliance between the Umpani and T'Rang! By talking to and freeing Rodan and Drazic, and then portaling them to their leaders, I was first able to convince Z'Ant to give an alliance letter and T'Rang Tracking Device to my party.
I then portaled to Yamir, where he accepted Z'Ant's alliance, and gave a Top Level Security Pass to the party. I then portaled to Mt. Gigas Peak, where I successfully attached the T'Rang Tracking Device to the Umpani Rocket, and blew the Dark Savant's Black Ship out of the sky! The computer affirmed that the Black Ship was indeed destroyed.
Having overcome many bitter years of war between the Umpani and T'Rang, I have finally formed an alliance, something never before done.
Also, I have struck a severe blow to my enemies. The Dark Savant no longer has his Black Ship. The Rapax King is dead, and his entire army at the Rapax Away Camp was wiped out. The Rapax Queen is MIA, as far as the Rapax are concerned.

I'm tying up loose ends, at this point. None of the Umpani have anything to say about the alliance. I talked to Panrack, Saxx, Bildublu, Kunar, Sparkle, and Balbrak at the Umpani Base Camp, and Rubble at the UTU area. Yamir dismissed me, saying he will see me on Ascension Peak. Also, the RPCs that I saved, Glumph, Rodan, and Drazic, are gone.
On the T'Rang side, there are only 3 left to talk to, but they have more dialogue. Z'Ant dismissed me, just like Yamir, saying he will see me on Ascension Peak. Sadok congratulated me on forming the alliance, then had nothing more to say. Tantris, in the Old Mine Tunnels, actually had a strange response. He first congratulated me on the alliance, then talking to him again resulted in him pretending that Drazic and Rodan were still with my party. He said something like, "I respect you Drazic, but for my safety, I can't be seen with an Umpani". Talking to him again, he says, "Please respect my wishes".
Anyways, Bayjin was only half explored, so I made sure to fully explore the island, taking out the Water Sprites on the mountain top in the middle of the island, and grabbing all the treasure on top, as well as the treasure chest in the NW, near the crashed ship. My Gadgeteer got to 80 base skill in Locks and Traps by deactivating the traps.

I've read that there's apparently some unfinished content relating to him whose remnants you might have stumbled across here.

Specifically:
* Apparently, he was supposed to have, as a personal weapon, a weapon called the Stinger.
* Toward the end of the game, he would give it to you (except that it's a different version with a higher to hit bonus), but at that point would no longer be recruitable.

So, perhaps he would have given you this weapon had that been properly finished.

Or, at least, that's what I've read.

I did another run of Bayjin, just to be sure that map had been completed. I re-checked the crashed ship, then circled around the mountain area, making sure to re-check the one treasure chest in the area. There were random treasures, nothing too important. I then re-checked the mountain top again.
I definitely made sure to re-check the 8 Rynjin huts, to make sure that I didn't miss anything. Nothing was missed. I am done with this area, as well as the constantly-respawning Rynjin and crabs.

I re-checked the Rapax Away Camp, assuming that it would be empty. Unfortunately, 3 groups of Rapax had respawned, and the Rapax Queen is still there. I talked to her again, and she said the same thing. From now on, due to an unfinished quest, I will assume that the Rapax Queen escaped to safety, and I will not fight near her. I did, however, cast a portal near where the Rapax Prince used to be, so I can explore in peace when I become Templar.

For now, however, there are only two paths: Finish the Mt. Gigas Caves unexplored areas, or explore the Rapax Rift. The former needs exploration (probably the most remote area of the game). I'm probably 90% of the way through the game.

The Sea Caves can be considered the most remote area of the game. To get there, you need to go from Mt. Gigas Upper Caves, to Mt. Gigas Water Caves, to Bayjin Shallows (fighting Nessie), to the Sea Caves. Or go from the Swamp, to Bayjin, to Bayjin Shallows (fighting Nessie), to the Sea Caves. Also, you need to crack the maze that is the Sea Caves, to get to Marten.
A close second would be the Mt. Gigas Caves, unexplored area. You need to join the IUF, and complete a few quests to even get into the Mt. Gigas Caves in the first place. Or you could be a T'Rang operative, and pay off Kunar for a fake Top Security Pass to get in (if you plan on destroying the Umpani Mothership). Or you could be working for the T'Rang, and have no plans to destroy the T'Rang Mothership, or pay off Kunar (having to swim from the Bayjin Shallows, through the Mt. Gigas Water Caves, into the Upper Mt. Gigas Caves, and finally, down to the Mt. Gigas unexplored area).

Anyways, time to tie up loose ends. This is the final map to complete before the last leg of the journey, the Rapax areas. I completely cleared out the "explored area" of the Mt. Gigas Caves. This is the smaller half of the map that is well lit, has signs pointing to destinations, and has Umpani patrols wandering around. I made it to the elevator leading up to the Mt. Gigas Upper Caves, where I took the elevator up, and set a portal in the safe area behind the closed door.
I then portaled back to Arnika, where I sold off all items obtained (I was getting close to blue encumbrance). Time to finish off the unexplored areas tomorrow. There are six chests to grab (I got 2 already), an instrument (Freeze Flesh), which is inferior to my Freeze All instrument, and a gadget that will let my Gadgeteer cast Detect Secrets for free, saving my Psionic and Mage a lot of Mental Realm mana, having to recast it so often (short duration).

There are situations where Freeze Flesh can hit enemies that Freeze All can't. In particular, Freeze All only hits visible enemies, while Freeze Flesh targets the same as Psionic Blast.

Also, Freeze All needs higher levels and skill to use reliably at higher power levels, and it is more expensive. (When stamina casting, higher level spells use more Stamina, though I don't know whether that's based on level or base cost. It isn't affected by power level.)

But there's only one class that has the capability to cast both Freeze Flesh and Psionic Blast, and that's even if you count items.

(Unless you use Scrolls of Freeze Flesh, but they're not buyable, though at least unlike some scrolls you can farm them from Rapax.)

Total success! I have finished the unexplored area of the Mt. Gigas Caves, despite a sign warning me to not go there (who's gonna stop me, the Umpani patrols who are in their "safe spaces")?
Anyways, I got all 6 treasure chests (the last one was guarded by the only set enemy there, a Mummy, which I got Mummy Dust from). I got a couple of useless spellbooks (note that my party has all spells in the game, so I sold them to Braffit for money). I got a P-Torch, which, when combined with the Magnifying Glass gadget, makes a Searchlight, stamina-casting Detect Secrets. My Gadgeteer is now like a Ranger, searching for hidden items for free.
Yes, I got the Freeze Flesh instrument, which I quickly sold. The reason being, that this is a MDP (Magic Damage Party). As said before, most of the time, you are out in the open, and would rather have a more effective, higher level spell available. The Bard, and Gadgeteer, only have 8 personal spaces for their instruments and gadgets, ready to use in battle.
For those rare instances, where you can only see the first enemy, and the others are around the corner, the Mage has both Freeze Flesh and Freeze All, enhanced by Powercast. The Psionic has Psionic Blast (it doesn't matter whether any enemies are visible, a rare spell). The Alchemist can cast Fire Bomb at enemies around the corner like that, just like the Mage can cast Fireball and Iceball.
So why would the Bard want to waste 1/8 of her personal inventory space, when she has a "hit all" instrument, and casters, armed with Powercast, ready to pick up the slack?