IMHO

Re-install windows on the faster raptor drive, and install all the WoWs and symlinks on the slower drive.

Why?

Remember folks, the game communicates to your hardware through Windows, basically your OS needs to be fast. WoW will also load reasonably fast if it is not on the system drive - it loads most things at start up and then additional 3d geometry and textures as you move around. Actually it writes very little, if anything, to the HD until you logout or exit the game.

This may not be the root cause, but I think worth a try.

Edit: spelling and grammar.