Dang... Sorry OP. What is happening to you is what keeps me mostly stock. I'd love to do all of those fun "Big Turbo" things, but I don't think there's a way to do it while keeping my warranty since it'll be pretty obvious that there were some things swapped out with the intent of boosting performance at the expense of reliability. It sounds like you are pretty capable with a wrench... what's stopping you from pulling the motor and putting in a used one from a salvage ST? I see them for sale on car-part.com for $2000 or less, and I bet you spend half that amount just for the Ford diagnosis. And that's not to mention the months that these things sometimes take to get resolved.