I hear you. Same exact thing Ford told me about a month ago, about my after market intake. They said it was messing up the reading and if i didnt put it back to stock i would slowly damage the engine. So i have been driving with my CEL on for 2 months now because of this problem. I dont know what to do about it.
Anyone have an idea? Would putting an after market MAF on solve the problem? They qouted me a huge amount for them to "fix" this problem. They also told me that they didnt liked the mods i did to this car because it wasnt made to be modded

. Anyways if you figure it out let me know..
Matt