I had the same problem, took it to Ford and they replaced the intake air bypass valve. I guess it takes a crap when intakes are changed. Oh well I hope it helps.
2000 CSVT #99 of 2150 Born on Date 9/28/99 17" Fondmetal 6700 on Nitto 450's 215/40ZR-17 PIAA 9006 Ultra Whites Eclipse 5443 deck Pioneer 6867'S all around No Big Mods yet still with warrenty.