Sitting here drinking my coffee, so I thought I'd give it a go and try to answer your questions best I could...You definitely aren't the first one to notice some of these plot holes in the game. For example, it always bothered me how, after George finds the tripod in the museum and goes back to tell Nico about it, they just move on from the tripod to discussing the Lochmarne Gem. I mean, I know there's a gem in the manuscript sitting on the tripod, but it just seemed to be a rather large leap of assumption...Especially since just a few lines of dialogue between George and Nico could have shifted the point of discussion from Pegram and the Lochmarne excavation to the gem. Instead, we get an awkward shift where George and Nico are talking about Peagram's excavation in Lochmarne to Nico telling George to go to Lochmarne to find the gem. Haha, it always bothered me. Anyway, on to your questions...
1. I always assumed the manuscript was sort of a visual map to finding the Sword of Baphomet. Not a map in the traditional sense. Rather, it contains a series of clues to locations and items which were needed to find out the location of the Sword of Baphomet. I believe the map was originally in the possession of The Templars, but they lost it when Pegram was assassinated by Khan. Remember, at one point, George mentions to Nico that he thought Plantard was a member of The Templars.
2. The guy working on a loom is symbolic of Spain. That's really all that image means. And the image of Baphomet is just that...Probably so a casual observer would be able to figure out what the manuscript was directing you to. Also, I believe there's an image of a church in that quarter of the manuscript...It looks just like the church at St. Ninian's This image is probably showing the viewer where the Sword of Baphomet lies.
3. Think you answered your own question there.
4. This is another thing that always bothered me. I don't have an answer for you. Seems if people knew what Bible passages to put on his tomb, they should've been able to find the children. Yeah, this part of the game always baffled me. I mean, it's not something that disrupts the flow of the game...It's just something you look back on afterwards and think..."Now wait, that didn't make any sense."
5. Flap and Guido were trying to get the manuscript back. So that's why they searched everyone who they saw leaving the hotel room...In case they were leaving with it. Think they knew who Khan was...They knew to look for him at the hotel...And they Flap kinda implies through George's questioning that he recognizes the guy in George's photo. But you do raise a lot of questions...If they knew who Khan was, why would they let him leave and enter the hotel without accosting him and finding the manuscript? Or why wouldn't they force the receptionist at the hotel to hand it over? Haha, never thought of this stuff before.
6. Remember, at one point, George makes the comment to Nico that Plantar was probably a member of the Templars. This is the most logical assumption, I think. The reasons he wants to meet Nico are never really explained, but I think that just adds to the mystery of the game. We'll never know for sure and that's just fine.
7. Haha, one of the great mysteries in gaming history. How did the Templars find the location of the sword without obtaining the items that George found and without being able to use the manuscript. Your guess is as good as mine.

Hey, thanks a lot for your thoughts!

At least, I don't feel like I am totally misunderstanding some key moments of the plot anymore.

I agree, none of these things interrupt the flow of the game, I only started to think more thoroughly about them once I finished the game again and again over the years. I just enjoy the dialogs and voices in the first two games so much.

Yeah, the first 2 Broken Swords are definitely the two best installments of the series. I was kinda disappointed by The Smoking Mirror when it first came out. I was playing these games in college and I bought them as they were originally released. But I do think time has been kind to BS2. Replaying it now, it's definitely not as bad as I originally thought. I think a big reason why it was met with kind of a lukewarm response is that it was released about a year after BS1. So most people had pretty fresh memories of the greatness of the first one and were expecting BS2 to measure up. Needless to say, BS2 isn't nearly as good as BS1.That doesn't necessarily make it a bad game. LOL took me about 10 years to realize that. In all seriousness though, Revolution could be making Broken Sword games for the next 100 years, and they'll never make another one as good as the first one. That's how great it was and is. I think it's the greatest point and click game ever produced.

I have the exact same feelings about the second game: the first time I beat it, I was underwhelmed. Seeing all Broken Sword games on sale here on GOG made me get all five of them and after finishing the first one I started the second without much excitement.

But surprisingly it gave me quite a few laughs, and I enjoyed it a lot more than I did all those years ago.

Yeah, I think your initial response is precisely what most people felt after playing BS2. It was a letdown after the all-around greatness that was the first game....But like I said, that doesn't necessarily make it a bad game. In fact, the light-heartedness and humor of the 2nd game is in many ways better than the 1st game. It was a good idea for Revolution to re-release these games. I think a lot of people are replaying BS2 and realizing that it's really a lot better than they remember. Out of all 5 games in the series, BS4 is really the only bad one. BS3 was a bit of a system shock, because the controls and dynamics of the game were so radically changed. I don't like BS3 as much as 1, 2, and 5, but I've come across people who enjoyed the 3rd one, so I think it's worth playing. BS4 was a waste. I actually thought that game might've killed the entire series, but Revolution rebounded (after more than 10 years) with BS5, which is probably the best Broken Sword game since the second one. I hope Revolution keeps on making more sequels.

I think its bc the main story is head and shoulders better in broken sword 1 but on the flip side I think the humor and jokes work way better in broken sword 2.

I'm going to be controversial here and say that BS5 was my favourite. It was a real slam-dunk of a sequel. Can't wait to see what they come up with next.

Ehh...I definitely think that BS5 was the best Broken Sword since the 2nd game...But to call it the best one...LOL, let's just say there'll probably be a lot of people who would disagree with you. But I was pleasantly surprised by Broken Sword 5. It wasn't a perfect game by any stretch and it had its faults...But it was actually pretty engaging, I thought. And the most important thing....It FELT like a Broken Sword game. I hope Revolution keeps on making sequels.

With the manuscript you have to start from bottom left. The knight holding the "crystal ball" with the inscription represents the by-eye visible piecfe of glass window you can see through the stone manuscript. It points the gathering place of the Templars which is below the cathedral, as the figure on the glass points.

Next you go upper left. It shows you need the tripod and the gemstone,and it shows a clue to get the final artefact, the Sword of Baphomet. The Bull represented either Baphomet, or the Bull Hill inSyria. Or Spain.
Either way at the location of the Templar Gathering pointed out by the bottom left you had to use the tripod and the gem to get to Syria.

In Syria was the Lense,so this gives a second meaning to the bottom left picture. You use the lense on the glass window of the cathedral to get the hidden image. Also gains the clue in Syria about England.
The burned head-templar leads you to where they dagout another Baphomet-statue with a mosaic before it. It gives the picture of the final location if you have the chalice from Spain through some convoluted reasining given right this point in the game by the journalist chick and André. Thus took full circleon the manuscript-map, also giving second meaning to the upper left picture which this time represents the Sword of Baphomet for good.

The upper right picture is likely the convoluted storyline of the Spain lady. André says something about "no self-respecting other knight would have that heraldic on his shield" or something, and that's pretty much it.

And (not sure if some people are aware of this), if you look at the manuscript in Nico's apartment after making progress in the game, George will comment as to what each symbolic image on the manuscript means.