Need Help On My 98 Gt 4.6l

Don,
The only thing that I can think of is cam timing. The modular engines are a PITA with the front chains and making sure everything goes back together just right. A compression test will definately show if you are a tooth off on the timing. The performance manuals say that you should dial in the timing to where both banks are producing as close to the same compression as possible.

Aftermarket adjusters are available and make things a lot easier to dial in. MMFF magazine had an article a few years ago on this and found that cars right out of the box could benefit from the after market timing adjusters. Their article found a whopping 40 hp on a factory fresh cobra, just by dialing in the cam timing! The correct way to get the timing just right is to pull the engine and use a degree wheel, but that is a major pain and the compression method should work just fine.

Good Luck!