I'd ask that you PLEASE take this advice in the spirit in which I intend it-- to try to help in any way I can after going through something almost identical (Really, do a site search. I'm not making this stuff up). I promised myself I'd stay out of this, but (apparently) I can't just shut up, so here goes:
I would not, under any circumstances, send that car back to JPS.
If, with the whole world watching, and magazine articles being written, and updates being posted, and before your final payment was sent, John didn't take the time to make sure the car was finished..... why in the world would he do a better job this time around? He's been paid. He's had his name in the magazine. What incentive does he have to make it better? Believe it or not (and I didn't for a long time, and it is truly a frightening thought)-- he probably did the best he knew how.
I've been told that the definition of insanity is to keep doing the same thing over and over, and expecting a different result. We all go a bit crazy when we want something really badly, and the end result falls well short of what should be reasonable to expect. I did. And I bloodied my head, banging it against the wall until I woke up and realized that I had already received all I was going to get from JPS Motorsports.
I'd get the car fixed locally if at all possible. You REALLY don't want your car sitting in John Steele's shop for any length of time (and sit it will).
Again.... forewarned is forearmed.