Did THEY remove and install the tranny?
If so, then you can almost guarantee they damaged something and didn't tell you.
I've seen this happen to my neighbors who then take it to me to figure out what's wrong with it.
The last one I looked at, they broke the shifter module that bolts to the transmission shift shaft.
The connector was so mangled from being hammered onto the electrical socket, that you couldn't remove it.
If not that, then maybe they stretched or pinched the wiring harness that runs up along the bell housing where it meets the engines.
Another 'rebuilder' didn't rebuild it right, and also didn't 'recode' it after installing.
So the kid (another neighbor) complained about shifting flare and slamming into gear.
It was a dodge that needed a DRB3 to code, and I guarantee that you won't find one of them anywhere today.
And the DRB3 'emulators' don't do that function, so the guy was SOL.
Rebuild (what quality, no one knows!) cost him 3200 bux!
I've seen all kinds of damaged stuff b/c the guys who do the removals/installs don't give a sh*t, and they just slam things together b/c they're stupid and ignorant. One has to wonder if they were former prisoners who all they did was fight and break stuff!
Although it will be a PITA, Like ToddZ said, one thing you can do is check for end-to-end continuity, short to ground and short to power on each of the wires that connect to the parts that are throwing codes. Maybe the rebuilders YANKED ON the wire harness before disconnecting it which caused damage?