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After 2 revs, the only synch signal is coming from the crank sensor. Time to go into PCM diagnostics.
 

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Will it run on just the JTEC, or does your build require the new PCM?
 

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Yes, the Jeep/TruckEngineController is OE. Wasn't sure if you have a standalone or piggyback. You may have a bad wire or connection, or crank sensor.
 

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The crank sensor gets power, then closes the ground path back to the ECU on the timing notches passing by. The ECU then signals to fire each cylinder coil pair according to the firing order - one spark before TDC on the firing stroke, the other pole sparks on a dead hole. If your crank sensor is swinging from 0-5V as it should, you have to confirm the signal is relayed successfully to the coil packs. You've already confirmed you have sequential fueling, correct? Both use the crank trigger reference. I've read about folks having connector pin issues in the injector and coil connectors.
 

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Dan Lesser is who I would turn to when attempting to diagnose/repair an ECU. I think he worked for Visteon, who were major automotive electronics suppliers and sponsors during the CART-IndyCar days in the early 2000's.
 

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I believe crank tooth count is 0.5:1 cam. Here is the stock JTEC functional overview:

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The cam sensor signal was almost a perfect square wave, 0 & 4V. The crank sensor signal has pairs of pulses, caused by the 54 then 90 degree separation of the cylinder firings. I didn't take a long enough sample to see a whole 720 degrees, but it's really likely that it's working right. I'll get a full 720 degree sample anyway...
It could be that the CKP signal could go to 5V if it was slightly closer to the high spot on the cam. The spacer that came with a new ones were just about the same thickness as a manila file folder. But as hard as they are to come by, it isn't worth the risk.
 

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That's great news! So there are 2 coil drivers? 1 can fire 5 dual pole coils, or the two can fire 10 individual coils - so you are just using the second one alone now?
 
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