It sounds like you got used to the mods and now it feels stock again. Maybe you should go test drive a new one and then get back in yours and feel it. Even if the computer did somehow "go back to stock" with your cams and other mods it will not run stock. Also it does take a while to order parts from Ford, it took 6 weeks to get my clutch and differential done.
2001 sangria zx3, best 1/4 time 15.70 @ 85mph. Now have an 04' Pontiac GTO w/LS1