It's pretty much "Grab files of character you want" (the files are numbered from 00 to 59, 00 being Synbios and 59 being Jane), copy into translation patch folder /files/s3/, rename to character you want it to be, then ran the patch to apply it to the game. There's also CFW##.CHP files, which appear to be for the characters you can play as (Scenario 1 has 00 only, Scenario 2 has 20 only and Scenario 3 has 00, 07 and 20, the same as the character ids of Synbios, Julian and Medion). Faffing with these made bad things happen though.
Anyway, the only noteworthy thing I've noticed so far is that there is a bug in Rogan's file - the first 2 bytes say exactly which character the file is for (it's basically the same as the ## in the filename). Rogan's is set to 36 (same value as Turk), when it should be 29. Fixing this hasn't fixed the sprite bug, unfortunately.
I need to do some testing and work out how these files work before I can do anything meaningful. I also need to work out how the enemies.chp (I assume) file works in order to grab Rogan's sprite out of it. I'd imagine it'd work in a similar way.