I know of 5 more (in addition to the ones mentioned previously - so yes the problem is more wide spread than initially thought) LSX Z's that have had their drive shaft bolts loosen, so as I've stated in the past, every Z that has done the conversion should verify their driveline angles.
As far as your comment on the half shafts... I was running the stock half shafts initially, and experienced the vibration. I then converted to 300zxt CVs and the problem was the same.
The John's Cars Tranny mounts that I've inspected are not consistent with the tranny heights (The mount bends are inconsistent) - Every one I've checked is slightly different... start there first - I'd bet your trans is up too high... Then side to side is probably off as well...
I'm really surprised this thread hasn't generated more concern - I see it as a huge issue with the JCI kit