If you're looking for LOUD (and don't have emissions in your state or can get around them), then go with an off road mid pipe. H pipes and prochambers sound the best with flowmasters although ive seen some people on stangnet say a "True" X sounds good too. With the 4.6L, shorty headers are worthless comparing gains to price and install. Long tube headers with a matching mid pipe would give u alot of power. If you can't get around emissions, then get a catted mid pipe or dump your exhaust after the mufflers.
I have an 04 GT that is pretty much stock other than a cat back system, i have the flowmaster 40 series with 2.25" all the way to the 2.5" tips. When i installed the system i was expecting a lot louder exhaust note. I'll admit it does sound better and a little louder than a stock system but over all am pretty dissapointed in how quiet it seems to be. I was wondering what else you guys would recommend doing to the rest of the exhaust system to get that extra noise level that im looking for. I was cheaking out the manifolds the other day and they look pretty small so im guessing headers will be in my future 
... Im pretty open to any ideas such as a new intake, some headers, x pipe whatever you guys feel would give me the loudest and best sounding exhaust tone i can get with bolt ons. Thanks 
