99 cobra minus the fix

Hell guys, I bought a 99 cobra in 2003 that hasn't had the fix. When I tried to have Ford fix it they told me that the date to have it fixed ended before I purchased the car. So, I was wondering if anybody else has had this problem and what they did to solve it. I've already switched out the exhaust except for the headers but I was wondering what intake I should look at.

Well, I guess I'm keeping the car now. I was planning on seeing how much power I can get all motor and then possibly spraying afterward. If not supercharge it. But, I'm thinking if I do that than I'll have to switch out the rods and possibly the pistons.