I have exactly the same problem on my bike. After investigating other issues I don't think I have an XT CDI (no wires for kill switch, side stand or neutral light) so I'm not sure about the state of the CDI. I have the manual and it explains how to sync the 2 carbs but it's different to what you guys have done. Now I'm really confused.

The TT CDI has something like 1 connector and 3 loose wires the XT has 2 connectors and 4 loose wires (off the top of my head - I may be way off).
Most of us start the carb tuning with the manual's method then tweak it from there.

I have started work on the TT again - I will be posting up again soon!