There is nothing wrong with the current GTE. You are doing a great work! :-)
But i saw the fix done by pSXAuthor in MAME, and it is reverse engineering applied to correct some problems in the GTE emulation.
I really have not seen the PCSX-R source code deeply yet and i don't know if it is useful or not. But i though it would be a good idea to share it here.
Cheers to everyone involved in PSCX-R, it is a really promising open source PSX emulator!!!. ;-)