Check Engine Light

[Mach.1]

I had a 80mm mass air flow system with a K&N air filter on my 96GT last year and everything worked fine. Then my intake manifold went out and I took it to Ford for them to fix it since it was a recall part. The next day when I got it back the check engine light came on. I took it back to them and they said they would check it out. They told me the the mass air flow sensory got shorted out by the oil from the K&N filter. They said since it was aftermarket they would not replace it. So I bought a new one and it did the same thing. I put the old sensor on with the stock air filter system and it worked fine. So I guess the sesory had not shorted out after all! Anyway it has been a year now and I wanted to try my K&N filter again. I put it on and it ran like a champ for about 2 weeks and now the check engine light is on. Does anyone know what might be causing this? Did Ford do something to my computer to make do this with a K&N? Just do not understand why it worked before but not now!! Thanks for the help!