Regarding PATS:

No, that's not possible.

You have to have two unique PATS keys, already cut. and then reprogram PATS from scratch when swapping out the PCM. You can DIY this with Forscan. IDS, of course, also works.

 

Have you checked the roller followers and cam lobes for defects? Hope you got her fixed by now but I woke up one day about 8 months ago and decided to take a large chunk of my quality of life away and go buy another Ford one morning.
I could probably pass as a master ASE mechanic regarding the timing kit replacements on the 5.4’s from all the literature I’ve read online. Other than the oil pump which you replaced, Ive read that faulty roller followers can issue similar symptoms as timing. Seems like you’ve flashed pcm, checked all vacuum for leaks, swapped coils, plugs, etc. If timing is correct, then possibly a defect in the cam lobe ? The roller followers have had issues breaking or springs loosing tension. GL

 

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i have the same issue. any updates? debating replacing all the coils here and the phasers. I see that you did the phasers/timing.

 

Hey, did you ever figure this one out? I have the exact same problem on a 2007 Expedition that has me stumped.

 

OK so I forgot to update this post on my final "fix". After all the chasing explained above, I cut the cats out of it and patched in straight piping and have been running it ever since without issue. The engine runs very well with the new front end and oil pump. I am somewhat troubled by my lack of troubleshooting prowess but can chalk it up to life long learning. I still need to complete the oxygen sensor patch to eliminate the CEL but the erratic misfires on the one bank are gone.

My apologies for the gap in concluding this post out.

Thanks so much for the guidance provided! Love the forums!

 

You could put a pair of high flow cats in to keep it legal.

 

It all depends on where you live. In some places, where there are strict inspection standards, deleting the catalytic converters is not acceptable. In some places, high flow catalytic converters are not acceptable. Where I live, catalytic converters must have a registered "executive order" number. Which means that I have to use an extremely expensive catalytic converter.