Another vote here for pulling codes. Your car is telling you whats wrong, you just have to know how to listen to it. http://dfwmustangs.net/forums/showthread.php?t=7908
FYI just because the check engine light is not on doesn't mean the computer isn't recording something. Run both tests , KOEO and KOER .
It could be as simple as the egr valve being stuck open .
Funny you replaced all the most expencive stuff first and completely ignored the cheapest thing in the whole tune up process, the fuel filter. This should be included in a list of items to be changed during a tune up.