Welcome to NICO!
You have stumbled on the best collection of early Q45 knowledge anywhere... I would browse through the articles at
http://www.Q45.org, and look through everything you can read here. Hopefully you replaced the timing chain guides on your replacement engine before installing it in the car. I suspect that's what cratered the first time?
As far as the the transmission, yep... it sure sounds like a transmission failure. I would lean toward having it checked by someone with a Consult to make sure that it's getting all of the signals it needs. You might also run the A/T self test (available in the factory service manual) to see what codes you get. If you don't have the factory service manual, check out
http://www.phatg20.net to download one... the earliest one they have is the 1994 version, but it will get you through a lot of things...
Just be sure to have everything warmed up first or the test won't work. Don't quote me on this, but I think that if it's the solenoids, they can be replaced from the bottom with just a pan drop. Not sure on that though...
Good luck!
Heath