My further messing with the henchmen presets has indicated that there is at least one factor I'm not accounting for and it is screwing things up- but I will say here what I know.
Changes to henchmen presets *are* reflected in existing saves; I have a save in the hall of heroes that I load up every time I want to see if one of my changes worked.
In terms of mods and dependencies, I am just using Blaze's four player mod as a base. But you could create your own mod from scratch using Bobbylein's guide:
http://www.larian.com/forums/ubbthreads.php?ubb=showflat&Number=504576#Post504576 as well.
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So from a clean, fresh install of the game, here is what I am doing:
1) Putting the four player base mod into Documents\Larian Studios\Divinity Original Sin\Mods... if you choose to use the four player mod too, make sure that you have the newer version of the mod (refer to this thread:
http://www.larian.com/forums/ubbthreads.php?ubb=showflat&Number=504225&nt=3&page=1)
2) Using Norbyte's unpacker's un-PAK function to extract the contents of Main.Pak into an empty folder on my desktop. Main.Pak is found in SteamApps\Common\Divinity - Original Sin\Data
As I understand it, if a mod contains certain files in the right place, then those files will be read/used before the base game files so that a mod can override anything. So when the game says 'what are Jahan's stats?' it will look in SteamApps\Common\Divinity - Original Sin\Data\Public\Main\Stats\Generated\Data.txt for that information. BUT if you are using a mod, it will FIRST check SteamApps\Common\Divinity - Original Sin\Data\Public\NAMEOFMOD\Stats\Generated\Data.txt for that information. In this case the name of the mod I am using is 4Player_-_Test_1ddd6993-6d9b-4e71-a437-1195dd217cf6. So any stats put into that second folder will be read first and used to override the original stats.
The pattern there seems to be that if you recreate file paths so that the name of your mod is an alternative to 'Main,' you can override things without editing base files (which upsets the game). So the henchmen preset files are located in Data\Mods\Main\CharacterCreation\HenchManPresets... following the pattern I made my own folder chain SteamApps\Common\Divinity - Original Sin\Data\Mods\4Player_-_Test_1ddd6993-6d9b-4e71-a437-1195dd217cf6\CharacterCreation\HenchManPresets. My thinking was that any .lsx preset file I put into that new folder would override the original preset. Anyways, short version is:
3) Creating a place to put my new henchmen presets that will override the old ones, in SteamApps\Common\Divinity - Original Sin\Data\Mods\4Player_-_Test_1ddd6993-6d9b-4e71-a437-1195dd217cf6\CharacterCreation\HenchManPresets
4) Norbyte's unpacker can open, edit, and save .lsb and .lsx files. So that is what will be used to view and modify the henchmen preset files which are all .lsx
5) Now comes the initial test, which is the success I reported above- I opened a random henchmen preset, changed their strength and dexterity values, and saved it (mind again that the .lsx being edited is a copy that exists in my mod folder; the original presets should not be edited).
6) When I opened my save in the Hall of Heroes, I saw that the henchman I had edited now had the strength and dexterity stats I gave him.
7) I started changing other things and it all went to hell and ARGH.
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So editing the presets SEEMS to be fairly straightforward. Different tabs, different nicely labelled boxes, everything easy to understand. It is a bit tricky to know the right names for things though- for example if you want to give someone blacksmithing you add points to "Repair". It would be really nice if somebody could make a master list of all the 'true' names of skills, talents, etc. I haven't been able to find most of them so I just guess what I think the obvious ones should be.
But there seems to be a problem depending on WHICH henchmen preset you choose to edit. For example, if I edit Ithalos, and then go to the Hall of Heroes, the Henchmen will endless scroll between a set of five henchmen, with bugged out appearances, and some of my edits will stay, and some won't, and it just seems random and unpredictable. If I edit Sondre, it is a little better but still somewhat bugged out, etc. This is especially weird because appearance data is stored inside the preset files, but sometimes when I try to edit someone their appearance in the game becomes totally different from what is set in their preset file. I have no idea.
I also experimented with adding a new Henchmen. There are 64 kickstarter henchmen, so I made a new .lsx file that was number 65 and added it to my mod folder. I copied another preset, but changed the name, description, etc. This actually worked, sort of- my new henchman did appear. BUT the weirdness with the order and number of henchmen available still happened. I suspect that it may have something to do with the ID number of the preset? I don't know how to go about creating a brand new ID for a new henchmen, which means I can't truly create one from scratch- my new one did share an ID with another preset, anyways.
*Possibly related*, but I noticed something else weird- Henchman #24 and Henchman #58 are both Ithalos. Identical presets.
Another weird thing, sometimes I get stuck in henchmen loops in the Hall of Heroes after trying to make an edit- so I can scroll through Henchman 1, 2 ,3, 4, BAM 5, 6, 5, 6, 5, 6, 5, 6, into infinity. Also if I scroll backwards (scroll = clicking the arrow buttons), then there are different henchmen, and different loops.
Edit: Another weird thing I should mention: if all of the henchmen presets are copied to the mod folder but *not changed at all*, then scrolling through henchmen in the hall of heroes will still bug out. The way I understand it, there should be NO difference between the game reading files in the mod folder and the original files IF the files are identical... but clearly there is a difference.
So... yeah. That should bring anyone reading this completely up to speed on what I've done, and observed.
