How loud is the clicking noise? Are you 100% positive it's coming from the transmission? Use a stethoscope type device to pinpoint the clicking noise. Wooden dowel works just as well. I'll bet that it's not the transmission, it could very well be an exhaust leak. Hoping not a lifter tick with a new motor.
On the motor side, get your vacuum gauge and timing light out and see if you can't get those numbers bumped up (advance timing should raise your vacuum). Test drive it and see if it improves at all.
Also, have you checked that your choke is opening and not stuck or hung up on something?? Wouldn't be the first I've seen that happen for sure.
Finally, where is your temp sensor mounted? Have you checked your gauge (ground out wire and gauge should peg out). Also, if you use thread sealant, don't use Teflon tape. It'll mess with the grounding. Use a liquid sealer if you need to.