Yeah, I'm sure you did all those things.
It may actually have ran. Ford is pretty good.
To work Well is another thing altogether.
There's ~10hp in just getting the factory combo tuned; if you do the 02 GTmaf and a dual exhaust with an x or h pipe, you can see a 20hp improvement over stock.
Regardless how you change things from there, other than adding a new intake, cams, or new heads, you are not going to improve HP from there; you've hit it's max.
When you change those things, it will need a tune, or it will detonate and destroy itself.
But then it's not stock.
At this point, little you do could surprise me at all.
Red '96 Cougar XR-7 240k mi. '02 4R70W, PST DS : '03 PI engine, 04 maf, 24lb injectors, 2.5" exhaust, '02 4r70w + Jmod, DirtyD0g TC + cooler + 3/8" lines, 255 walbro fp. Alpine system.
Black '96 Cougar XR-7 (Lazarus) 210k mi PI Intake, '02 4R70W, Jmod, PST DS, GrogTune, Konis, Mark LCA+Poly, racecougar Custom Engine Chain, and JL and racecougar Bracing.
Black '97 Tbird Limited Edition, '02 4R70W, 255 walbro, PST DS, PBR Brakes&SS lines, Toicko Blues & Springs, GrogTune.
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