i know this might not be much help, but i was tearing my hair out trying to figure out this and that on my WarpUP Warp3D config. nothing would work. PPC exceptions all over the place.
my install was 3.9, with the version of WarpUP off the 3.9CD, it is the latest version (?apparently?)
got hacked off and installed the version of WarpUP (V4.0) off of my HereticII CD and the version of Warp3D off of there. thinking about it, there was no way they would distribute a game with an unqualified mix of drivers surely?
it worked! version 3 of warp3D and WarpUP v4 running fine.
Heretic2 works,
WipeOut2097 works,
Truereality N64 works,
GLQuake works,
Warp3D demo works,
WarpOS Meter (ppc cpu meter) works...
upgraded warp3d to version 4.2, much better speed. but left WarpUP at version 4. not set to compatable mode during the install...
i've also installed blizzpatch off of aminet that disables the PPC.library on startup, and set memory protected to "yes" using warp prefs.
i have no idea if that'll work for you and your drool worthy setup, but just an idea.... i hope you get it nailed down soon :-)