3.5 Ecoboost swap without a spark

I swapped a '17 3.5/6R80 out of an Expedition (Gen 1 still) into a 2001 Reg cab 4x4 truck. I had a guy do the harness and he sent it back to me and much to my surprise it started first try on the garage floor. Went through the mechanics of the swap and it ran absolutely great for FOUR years! Never left me stranded once...until two months ago. Just like someone reached over and turned the ignition off. Still had power everywhere. I immediately checked for codes - nothing. Towed it home and figured it would be a fuse or something simple. Well...that was two months ago.

I have never had such a nightmare as with this thing. Everything I check turns out fine. Power and grounds to the appropriate pins at the PCM, check. Power and ground to the coils, check. (also while cranking) No shorts to power or ground on that circuit. No spark on any cylinder.

Alldata symptom based diag process says to check VREF to the throttle position sensor. Check. Then check for RPM to display while cranking, check. Then check for Cam/Crank Sync PID while cranking. Check. Then check the ignition circuit. Done. Twice. I can take a +5v signal to the signal wire from the PCM to the coil and manually get it to spark. The PCM isn't sending the signal. OK. Maybe its the PCM. Bought a used one, PATS deleted it (verified by Forscan), crank no spark. Thought that maybe, maybe, maybe that PCM was bad. So I bought another one (luckily they are only $40 on Ebay) Swapped it in, PATS delete again. Same result.

I am 99% sure it is getting fuel (I can smell it out of the exhaust after cranking) and rail pressure reads above desired. I don't even think this matters though, because the PCM will make spark without fuel.

There are four DTC's, but they have been there for 4 years and I doubt they are going to cause this. One Ambient air temp sensor fault, one PCM Power on timer fault, one Generator current sensor fault. I've been told these are common in swaps and not something that would keep the PCM from making spark.

So I am really, really, really stuck. I have no idea where to go or what to do next. Anyone on here have ideas or things to check?

I think your tune is corrupted, Have you ever tried to get it back to STOCK with IDS/FJDS?

I'm surprised it runs right at all with no ambient temper sensor, that's one of many temp inputs the ECM uses for Speed Density calculations

So I turned to Jem-Sport to diagnose this issue for me. He went through things and learned that the PATS delete was done improperly. The PCM is en route back to me now and I expect it will start and run as it should. I can only assume that a bad coil caused things to fail initially and I have replaced all of the coils to be safe.

As for the ambient temp - in Forscan I can see the proper ambient temp reading, but for some reason it produces a code. I wonder if the PCM uses more than one sensor to get this data and maybe the other sensor isn't available. Either way, the truck ran great prior to all of this.

I scoped the crank signal. Found one missing tooth signal. Took a borescope to the CPK sensor. Sure enough, a bent tooth (just barely) on the reluctor wheel. This engine and trans has never been apart, so I have NO clue how this happened. Some one dropped the wheel at the Ford factory and it took the CKP 60k miles to lose sensitivity? I pulled the trans, bent the tooth back and the truck starts.

RPM showed normal on the scan tool, but apparently you can get RPM and still have confusion as to where TDC is. No code for that, apparently!

Solid diagnosis!