I'm no transmission expert, but they are separated from the rest of the work you had done, so I dont see a relation. The synchros in the Z are known to have issues.
Does this happen all the time, or only under certain circumstances? My 6th gear synchro grinds if I try and power in to the gear. If I press the clutch, wait a second and then shift, it works fine.
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~Rob 
-DD Air Guide, Stillen G3 CAIs, 63mm Throttle Bodies, Motordyne M370, Berk HFCs, FI TDX CBE (non-res, CF), Sprint booster v3, Ecutek Dyno Tuned, and the list goes on...
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