So far this is what we have done: 1.Did a long block overhaul on a 2001 Jeep 4.0L straight six. 2.Changed rings, pistons & connecting rods, head machined, valves good 3.Changed cam shaft and bearings 4.Changed Crankshaft bearings, clearance good on bearings, reused flex plate. 5.Changed camshaft position sensor, old one had a loose magnet. Voltage into sensor +5VDC, GND verified 6.Changed crankshaft position sensor, verified circuit good, output triggers ASD relay. 7.Verified 42psi fuel pressure 8.Changed coil pack, seems like we have no spark. 9.Checked codes, no codes showing 10.Cranks fine but not even a kick. 11.Checked camshaft position sensor alignment at TDC, even tried 180 out. 12.Swapped computers PCM/ECMWhen we first ran the engine it started right away and had a rough idle. Checked and cleared all the codes, mostly bad grounds and old wiring. Started the engine several times and we were in the process of troubleshooting the rough idle. Engine finally started good and idled perfect, turned it off and can’t get it to restart. When key is turned on fuel pressure comes up then the fuel pump drops out after a few seconds. It seems like the crankshaft signal isn’t getting to the computer but it is because when it activates the ASD activates as well as the fuel pump. Suggestions?

 

Pull the crank sensor and see if it got damaged by the flex plate. I'd even try swapping out the old crank sensor.

 

Also, the crank sensor has to be damn near perfect for it to work, but this is from the service manual:

"the ASD relay will be de-activated by the PCM if there is a crankshaft position sensor signal to the PCM that is lower than pre-determined values"

Lower than predetermined values might be enough for the ASD to trigger, but not enough for spark to occur.

 

I swapped an engine in my XJ and went through hell searching and throwing parts at it.
It ended up being the crank sensor. I'd be shocked if it was anything else

 

That exact thing happened to me when I installed my motor. It was my first time installing a motor and I was by myself. I got it lined up but it took a little more wiggling than I thought. Went to fire it and it just cranked and cranked but wouldn't even try to fire. As soon as I pulled the crank sensor you could see where the flexplate made contact when I put the motor in. I put a new crank sensor in and bam, fired rite up.

If you have confirmed that you don't have any spark on any of the cylinders, i would try the crank sensor. Goodluck