Biggest, you ran into the same problems the first LT headers guys did.
While our PCM's with the Smith Predictive Software is pretty sophisticated, the files for the engineering models can only be so large.
Also the throttle responses are in direct correlation with the thrust output of the transmission and throwing 37" tires on is not going
to allow the transmission to be at the thrust level that the Tune was designed for.
The only reasons Whipple has a Tune for the LT Headers is that they went back
to the Ford's Tier 1 engineer with a Truck and commissioned him to design a new model for LT Headers.
And the cost of that, Whipple says they probably never recoup the cost of something like that.
And all of Whipple's Tunes are highly encrypted and most likely will never be crack.
I'm sure when you talked to Whipple they did tell you that you would need a third party Tune for the 37" tires.
The Tunes from Whipple are based on a stock Raptor with one of them being for a stock Raptor with LT Headers.
Both being certified to pass state inspections with the exception of California, that is still pending.
There is a little room to wiggle in the Whipple Tune such as CJ 500 Twin 65mm TB and going with the smaller pulley (3.675) but more than that and it's Dyno time.
You are the first to try 37" tires with a Supercharger any make.
Have you thought about changing gearing ratios to bring your setup closer the capability of the Whipple tune?
Also to point out without changing the gear sets you're going to have a hard time seeing 500 rwhp with those 37" tires, to much mechanical loss.