Pages 31 and 32 of the manual do not provide enough information about identifying an item.
For example, how do you know how much you are going to be charged to identify the item? The space where this information is supposed to appear is filled with some sort of weird red graphic, and I get a warning message saying something like,
"Are you sure you want to pay more for this item than it is worth?" More? I'm not seeing ANY amount listed that I would pay if I authorized the transaction.
Is there any clue as to who charges the least for the service of identification?
Thanks.

If you're getting the message 'Are you sure you want to pay more for this item than it is worth' that means you are bartering, not asking a trader to identify the item.
If you switch to the 'identify' tab on the bartering window and then click on an unidentified item on your inventory, you'll get a 'are you sure you wanna do this' kind of prompt and in that prompt there will be displayed the ammount it will cost to identify the item in question.
Same thing for the repair tab on the bartering window.
As for who charges the least, i have no idea. The more you trade with someone the better prices for bartering you'll get, maybe same thing goes for identifying and repairing items, but i'm not sure.
And btw, manuals are not meant to be substitutes for actually playing the game and trying out stuff for yourself.
And couldn't you just have made a single thread for all these questions ?

I clicked on the "Magnifying Glass" icon, the column for the person I was dealing with was filled with a weird red graphic, and.....you know the rest.
As for posting all of the questions in one thread, that would have been a huge mistake.
I've tried it before, and the persons who answer don't bother to make it clear WHICH questions they are responding to, even when I label them with numbers. This way, there is less confusion.

Regarding the confusion in multiple question threads, you can always press people, in a nice way, to be more precise with their answers, but i guess i can see your point.
As for the bartering window, i'm unsure if you managed to identify an item or not.
The weird red graphic means you're on 'identifying items' mode if you will. From there the only thing you have to do is make sure the item you're selecting on your inventory is an unidentified one.

I can't even remember how I managed it, but more or less by desperately clicking at random numerous times I finally lucked into a message that said what it would cost to identify an item. Like most games, this one is completely NOT intuitive or user-friendly.
This means that all the world-building is completely wasted. By pissing off the user with a clumsy interface, you yank the user back into the crappy "real" world.

The best way to identify (imo) is to invest some skill points into the Identify skill (Survivor skill 'tree'). This will allow you to automatically identify items of X level and below when you pick them up (X being defined by the level of your Identify skill).

See this post for basic explanation of buying, selling, repairing and identifying items.
When learning to use the window you must have entered a value which is more than what the merchant wanted for the item which causes the "Are you sure you want to pay more for this item than it is worth?" This is useful when you are trying to increase the merchants opinion of you in order to get better prices. You might also have offered him items without pushing his scale button which "gives" him the items instead of him having to pay, this also increases your standing with the merchant.

1 - You engage in bartering with a trader
2 - There's 3 things you can do while bartering: 1 - trade, 2 - have items repaired, 3 - have items identifyed.
2.1 - By default, when you engage in bartering, the default window you're on is the 'Trade' one, meaning that if you wish to have items repaired or identifyed you'll have to click on the appropriate icons (on top, magnifying glass for identifying, hammer for repair)
2.2 - BUT, not all traders or NPC's are able to repair and/or identify items. In those cases you can't click on the greyed out magnifying glass and/or hammmer, and you'll have to find another trader or NPC, one who does offer the identify and/or repair services.
3 - If the Trader/NPC you are currently bartering with DOES offer the 'Identify' service, you just have to click the magnifying glass icon, and then on your inventory click on an unidentified item, and it's at this point that the window showing you how much it will cost to identify the item pops up.
Surely, this isn't really that obscure or cumbersome is it ?

Note also that when in identify mode, in your inventory, items that need to be identified are shown with blue names. If you click on an item without a blue name, it doesn't need to be identified, so nothing will happen.
As for the cost, if they like you 100 percent, it costs 100 gold. I think it scales up to 300 if they don't like you much.

Look bearcat33 i don't know how simple we have to make it for you to understand so here is the basics. When you talk to a trader, click the bag for trade, it takes you directly to the trade pop up, in there you have your items and his/her (trader) items at the top of each side you see a number, that means the current value of all the items including money, that each one of you currently have. Closer to the top you see 2 icons a hammer and a magnifying glass, these two icon represent an action, the hammer is to repair an item and the magnifying glass is to identify. When you click the hammer some of the items values will turn red, this means that you can repair them for a price, remember the value under the items is the value of that item at that current condition, for you to know the price to repair it you have to click on it and check how much it costs, prices range depending on the quality of the item and if it is identified or not, basically repair prices are always different. Well that's all there is for the hammer icon, now for the magnifying glass u click on it and some of your items values will turn blue, that means that it has to be identified, you click on the item and it will always tell you that the price of the item identification is 150 gold, it always is the same price no matter what kind of id level it needs. Finally after you checked those icons and you wanna get back to the barter menu click on the icon that shows a hand holding a coin purse. Really is not that hard to understand, it is pretty simple and obvious once you get the hang of it. Also man if you don't really get it, and still you do not understand please give up on rpg's. Not joking thought man, it is really easy.
P.S. some trader can only do specific actions some can trade and identify and some can sell or buy, and a few can do all three.