Is there anything that the trans guy may have disconnected taking the trans out. I
Depends if he just removed the transmission or removed the engine and transmission.
The wiring between the the PCM and the engine fusebox does not have connectors that I can think of.
Check that the PCM connectors are plugged into the PCM fully. (maybe he did some wire testing to the transmission?)
Normal diagnostic testing procedure is called "half point checks" So the " half point" is the relay(s) socket.
With the key in run use a volt meter to check each socket for two +12V contacts. (coil power and fan power).
I am not sure but under most conditions unplugging the waterpump temperature sensor(for PCM) should force the PCM to ground one pin in the relay socket to activate the relay coil. You may be able to hear or feel the relay "click on" if someone else turns the key to run or starts the engine. Meter probes may not contact the socket contacts properly. Something small and thin like the relay pin will make good contact. IE a male quick connect.
If everything at the relay socket is functioning (active relay and good power) you have probably eliminated the relay and PCM.
The next easy point to check is at the fans. Use a test light. Unplug both fans and use the battery negative for the clip end check for +12V at each fan connector. If you have +12V change the clip to the battery's positive post and check each connector for ground.
Assuming that all tests are good the fans are bad. Do the fans spin freely? If + or - is bad at the harness you have some wire tracing/checking to do.
Note: Just because a meter shows good battery voltage it does not mean the wiring is good. There may be enough power to give a good meter reading but not enough to run a fan. Corrosion in wires or at connectors can make testing difficult. The above are the easy checks and corrosion and wire damage can require more testing to find.