Modding on linux is a little finicky. For all Beamdog's edition, I wrote a script[1] that would symlink datafiles as a lowercase version everywhere (unless they were already lowercase). After this, all WeidU mods were working okay (at least for BG I&II). I have P:TEE but never modded it however, but the process should be relatively similar.

[1]: http://pastebin.com/raw/nmkSGj0L

Another option is to setup a FUSE mount for a case-insensitive virtual FS. I remember having to do this to get Civ5 mods to work.

tolower and related things I'm comfortable with - the main question I can't answer is where do you run the weidu mod?

Sorry, indeed this can be useful to know.

You must run weidu where chitin.key is