cobrayankee: I"m just brainstorming here but it could possibly be the fact that you are running with the off road h-pipe on the 4.6. Is your "check engine" light coming on much? could be your emissions system messing with the engine. I don't know if you are using the MIL eliminators or not. Plus that's alot of backpressure loss w/out those cats but I'm not sure completely of it's significance. The only back pressure you have right now are the flowmasters. Just some thoughts.
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FOR SALE: 1996 Mustang GTS: 5-speed, K&N, removed air silencer, 3.73s, 48,000 miles. $11,500
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