Loss of spark after running for 5 minutes

[BlakePorterMcLain]

Hi, I have an 04 Expedition with the 4.6. Recently did an engine swap and it ran fine at first, but randomly started doing this thing where it loses spark after about 5 minutes of running. If I disconnect the battery and let it sit overnight it will start right back up and do the same thing. I know I have fuel, as I can smell it when cranking, and when I spray starting fluid in throttle body it doesn’t even cough. Replaced all 8 plugs. I will note that my CHT sensor is not working, but I don’t think this has anything to do with it because why does it start back up after sitting overnight? Picked up a new PCM and now it cranks but no spark at all, still have good fuel. Any suggestions are very much appreciated. Would also like to note that the relays are not overheating, and I have switched them around with known good relays.

 

[whtbronco]

Well the CHT sensor is used by the PCM and it appears if the PCM doesn't get a signal within range it ca put the vehicle into limp home mode.

Any codes present?

My first thought though was a poor ground, there are a couple grounds under the hood. Now that I have thought it for a minute I'd check the crankshaft position sensor wires and verify the connector is properly seated.

Here's the grounds for my 2004 5.4L, but the grounds are likely the same or very similar.

 

[DieselMonk]

Crank shaft position sensor, cam shaft position, immobilizer and their wiring harnesses