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I recently replaced the engine in a 1999 GT with one from a 2004. The engine I removed had a Kenne Bell, and other supporting mods, and a custom tune is on the computer. The car won't start and remain running. It sounds as if the timing is too far outta whack. The 04 engine is bone stock. I have checked all the usual suspects, Crank & cam sensors, gem, CCR, etc. The only remaining mod on the car now is a 325 Aeromotive fuel pump. Now, I am aware of the PATS...could I upload a stock tune file with an SCT tuner, and not interfere with the key programming? I have also read that Ford changed the platform, or operating system of later models like the 04. So is attempting this with a 99 computer a waste of time? I've attached a photo of the label on my stock 99 computer. Appreciate any insights! Thanks!
 

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I'll be honest, I'm not sure about the 99 to 04 computer difference, but I received my 01 Bullitt with a 93 octane performance tune, but no tuner. I contacted BAMA performance, about a stock tune and they said they didn't have those, that I would have to go to my Ford dealer to have my PCM flashed. I did find some eBay listings that will do this as well. How this helps a little.
 
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