Austin97

I'd say take your cats loose. It ran fine before and doesn't now. Might as well rule them out.

00gstang

compression test and make sure the engine is still good

then check your exhaust for leaks

BolletuH

4.6L PCM with a 5.4L PI Engine... I don't like the sound of that at all. Unless you reprogram that PCM it will think that the engine it's working with is a 4.6L Non PI period. Have you reprogrammed or will you need to do a PCM swap?

ghostrider

It sounds to me like the timing is of or as others have posted a fuel issue

ColdOne

I did the same swap, from 97 4.6 to 2001 5.4. I used the 5.4 wiring harness with COP's instead of 4.6 coil packs. Original 4.6 PCM ran exactly as this sounds, like crap. Took computer into dealership to reflash and reset for the 5.4 ( Luckily I have a friend that owns the dealership so saves $$). Flashing the computer wasn't easy. Service tech said it couldn't be done, but when I said I would order a new 5.4 computer if it didn't work, he worked with me. ( again I know the owner, it helps) downloaded 6 different programs before we found the one that runs my truck. Lots of other issues resolved with the swap, but this was the hardest.

00gstang

I agree with ColdOne. The 4.6L engine is entirely different than the 5.4. Timing variable are different, different fuel trims, different MAF ratios, different IATs. It would be wise to use the 5.4 wiring harness and PCM. Ford used two different PCMs for a reason ....

Austin97

It's the same PCM. Different programming, like coldone did to his. I'd think the 4.6 tuning would be able to adjust, and I've read in write ups that it will but he's the one who actually did it, first hand experience wins. It's not that hard to reprogram if you have a 5.4 truck there you can copy the as built data out of.

lowce805

My battery died from cranking it so much..
I disconnected my POS terminal and started to charge my battery I reconnected the battery and set the charger to "12v Start" and the truck started up fine.. drove it around and seemed perfect 1hr later it slowly started to get rough and a little longer I heard that missing sound again.. I parked it and now I'm back where I started..

Justin251

Alternator?

lowce805

Knock Sensor? maybe..?