Well, made things easy on myself and just added a "rename" function to the extracter tool instead.
Using LDoN skeles in place of classic mostly works. Only trouble is that their sit and stand animations appear to get reversed, so they collapse into a pile of bones as they get up and uncollapse and freeze into the first frame of their standing position when sitting. Things straighten out as soon as they move, at least... Could probably fix that one way or another but more work than I care to put into it at this point. Oh, and the alternate textures don't work for whatever reason.
Instructions for nobody:
1) Copy skt_chr.s3d (LDoN skele file) and rename it to ske_chr.s3d
2) Go to ske_chr.s3d in the extracter tool, right-click the SKT_ACTORDEF bit that comes up in the other column and select "Rename Model"
3) In the rename popup, change SKT to SKE
4) Put ske_chr in your global load file above global_chr and/or global6_chr
Made me realize that the extracter tool currently misses alternate textures and particle data associated with a model. Might fix later.
edit:
Replacing one model with another globally is much the same:
1) Find a file containing the model you want (
this list is a good place to start if the model you want is not already global, otherwise it's probably in a file with "global" in its name)
2) Copy that file OR extract the desired model from it.
3) Find the 3-letter identifier for the model you want to replace (above list helps there too)
4) In the copied/extracted file, rename your desired model from whatever it's 3-letter identifier currently is to the 3-letter identifier of the model to be replaced
5) Put the copied/extracted file high up in the global load file (first line is fine)
If you have texture caching on (I think?) sometimes some of the original model's textures will show up instead of the proper ones. Should sort itself out, else you can delete the texture cache files.
Cazic Thule snakes work, other than having a bizarre kick animation (kicks his entire model at you). At least the cazic from unrest_chr, didn't try the one from fearplane_chr.
Making non-global replacements would also be doable, but more work to set up.