Help me diagnose last couple bugs on the swap.

I need some help diagnosing the last couple issues on my magnum swap. First, let me list my setup: 1994 5.2L out of a Grand Cherokee, factory pump mounted in the tank, fuel regulator is the factory style on the rail, PCM is from a 94 manual trans Ram, using an AX15 transmission. Intake plenum is fixed. Everything is basically stock.
New stuff: plugs, wires, cap, rotor, IAT sensor, Coolant temp sensor, Idle air valve, MAP sensor, O2 sensor.
EVAP is removed as well as EGR. Injectors and rail were cleaned. Cam sensor has been sync'd.
Codes from the PCM are for AC fault, EVAP and EGR.

I have two issues with the performance:
Cold start seems to crank longer than typical before it fires. If I shut off and restart within 5 minutes, it starts as normal. After an hour, it cranks long again.
Second problem is during acceleration, the motor hits a certain rpm and feels like it loses power. I don't have a tach so I don't know what rpm.

I think it could be one of three things: Not enough fuel, weak coil or PCM issues.

Here is what I've tested so far:
Coil resistance readings are out of spec, but it still gives a bright spark.
Fuel pressure is 32 psi at idle, the FSM says that is correct. At idle, I pulled the vacuum line from the regulator and the pressure went up to about 39 psi, which is in spec. I tried reving the engine and the pressure went up slightly. When I shut the key off, pressure drops to about 2 psi within a couple minutes. I have not tried a capacity test yet, so it is possible the engine is starved for fuel at higher rpms.

What should I test next?