Hey hows it going! I live on the peninsula and go over to the east bay all the time, so Its nice to see a fellow bay area Q owner.
So just to be clear you can shift the car normally when putting it in 1, 2, or 3? In the service manual there is a section for how to run the AT Self diagnosis which will show any problems if it finds any; in the 94 service manual it is on AT-41 which you can access at:
http://www.nicoclub.com/FSM/Q45/1994_Q45/at.pdf
Dont worry the cars are similar to where the only difference is that the transmission starts in second gear rather than first for the 94 based on the Transmission control unit. You can replace the TCU with a 94 if you wish.
Now really your best bet is a JDM transmission as they are typically very low mileage; almost always less than 80k and average around 50k. There are a few importers in the bay area but I dont have any experience with any of them. Sometimes a transmission pops up on ebay for $300 plus $150 shipping where you need a shipping address with a forklift, which is not a problem for me because of my dads work.
I would be glad to help if you need it.