The Thunder II has a 2 humbucker config with options for phase and coil-tap
and maybe an active circuit with a switch to activate.
http://www.westone.info/thunder2.html
You're in luck.
The Westone site has wiring diagrams for the Thunder Series.
http://www.westone.info/wiring.html
Thanks to the diagram contributors.
See if you can match your setup to one of these.
Anyway they will get you moving in the right direction.
What exactly is it that you need to do to the guitar?
One of the electronic wizards here may be able to give you some tips.