Thanks everyone for the suggestions. I'm going to start from the cheapest to the most expensive. I'll start with changing the fuel filter again and tossing the stock airbox and filter back just to see what happens...If that doesnt fix the problem, then I guess I will change things I have not changed like O2 sensors then fuel pump and lastly the CAT...

Wait...but I dont think the CAT can be a problem because if its clogged, then the car shouldnt sometimes run really strong should it? It should always be bad no? I mean it should just be clogged right? Are there any tests one can do to try and diagnose a clogged CAT?

PS. I was running the Ford AWSF 32F plugs which I run all the time. As a test I tried other plugs but same results...Its just annoying because its so inconsistent.