What could have happened?

[Rev]

When you put in a new tranny it will have a new oil seal at the rear where the drive shaft goes in. You should put something like wheel beartng grease on the drive shaft yoke splined tube that fits into the tranny. Otherwise it may run dry for awhile enough to mess up that rear oil seal. Leakage would bleed out the rear seal and onto that drive shaft yoke tube where it would be spun off and on to your cats causing the smoke. Just a possibility.

Rev