[CageFighter_Dan]

the main issue here though as well wil be conflict with transmission if it is not the same in your original truck as it is in the donor truck ie. w4r70 which is in almost all 4.6l that i have seen , and w4r100 in all the 5.4l if your truck has a different tranny it is not a simple tune issue either at this point.as for ford not willing to reflash the pcm to a 5.4 tune, that is exactly why i went with the gryphon and bills custom tunes, with this it has the ability to rewrite/flash your existing pcm for the 5.4 flash and running program just like it was already a pcm from a 5.4l truck. the benifit of doing it this way is , you will still have your exisitng hook ups and factory set up for your transmission and no issues with it down the road, as well as your stock pcm pats settings programmed for your key already. I suspect that that is another issue that he is still using the original key with the pats transponder in it from the original truck but attempting to start the engine with the new pcm which has not been scanned and programmed for this key, the other issue i mentioned before which is quite easy to over look, "i did and put a new fuel pump in the truck because of it" was a blown 30amp mega fuse ini the engine compartment that controls over all power up to the pcm , and with it working on my vehicle gave me the exact same symptoms of a pooched fuel pump assembly, i changed the pump then after realized the fuse.Like i was mentioning at the beginning , use your stock pcm and harness and use the gryphon for a stock pcm flash to 5.4 settings from the 4.6 ones and it will save you alot of grief down the road, this all that you are experiencing now, is that same said grief that i was trying to prewarn you about before the project took off, ford as well told me when i was in the planning and searching stage of my project that i would also have to change my pcm and harness to match pcm, after more research and not just taking their word for it, i found out from others that had done the actual swap successfully that i could use my stock and was better off to do so to prevent potential conflict between pcm's and sensors from the swap. That it is easier for a tuner to reflash/program a stock pcm then it is to track down all the other stuff from the donor vehicle to make it work with the swap set up. With this there would be no need to change clusters/ tranny/ key transponders, coding for said key, and other compatibilty issues. But i have mentioned this at numerous accations, and at the beginning stage of your swap. Don't really know what more to say other then smack your mechanic upside the head and say LISTEN TO WHAT I WANT , not what you think needs to happen or what ford themselves tell you . Ford does not support doing the swap since they will not touch any aspect of it due to liabilities of engine and component reliability warranty. This is why no one sends their trucks to ford in order to do a swap like these. I have found from personal experience that ford was very reluctant to give any advise or service work in any way with my truck once i mentioned the project i was undertaking. But i will leave this responce as this with a quote i learned from my grandfather and find myself leaning against quite often as i get older " Learn from other peoples mistakes, cause you won't live long enough to make them all yourself"