Bablyon,
If you don't get an answer from this forum, the Yahoo! EQ6 or EQ6Mod forums. EQ6Mod bypasses the synscan handpiece and controls the mount from a laptop/PC (I am going to try this using the new V3.23 PC direct firmware but other members of the EQ6Mod forum have stated the PC direct mode still seems unstable).
Only problems I've had with my EQ6 have been caused by incorrect levelling of the mount. I fixed this by making a levelling plate so I can accurately check the mount level after the scope is mounted. That said I haven't got around to drift alignment on the EQ6 yet.
You can get the instructions for the plate at
http://members.iinet.net.au/~garin/EQ6plate.pdf )unfortunately it's 536K so it wont upload.