theory #1: coolant temp sensor: possible, I did not change this from the old engine to the new one. Where is it?

theory #2: idle screw: unlikely, since both the old and new TBs exhibit the same problem.

theory #3: EGR valve: possible, Is the EGR valve the very simple ball-in-tube valve that inserts into the top of the valve cover? If so, I installed a new one. If not, where is it?

 

I swapped both sensors on the front of the intake manifold (green connector and black connector) from the original engine into the new one. The problem persists. I think at least one these is the coolant temp sensor, so I think we can rule that option out.

Perhaps EGR is the cause. I need to figure out where it is and swap it between the engines.

 

your egr valve is in the back of your engine, next to your firewall. Looks like a spaceship.

 

Both sensors are coolant temp sensors- one for the ECU and the other for the cold start circuit.

I keep reading along the lines of "cold started in the morning and was fine".
The idle and timing both need set when the engine is at normal operating temp / warmed up, not on a cold engine.

Honestly, it doesn't make a big difference how it idles when cold because that is a different operating state that depends on how the engine operates when warm.