My son has an 01' SS. Car runs great and starts fine cold. The issue is, after the car has warmed up to temperature, it won't start again unless you wait 15-20 mins to cool down. It will act like it wants to start with a few cylinder hits but nothing. Only thing I haven't replaced on the engine this year is the TPS. My son (just an 18yo kid) works at Ford and even had the techs there look at it with him with nothing found. They smoked the intake and found no leaks. All hoses look good.

No codes
New:
intake
Seals
Wires
Plugs
Coils
Egr
Cat
Mass
O2
Coolant sensor
fuel pressure regulator

 

I believe the no start after warm is related to the crank position sensor. I could be wrong but that should give you somewhere to start looking. Doesnt sound like a vacuum issue, it would be present regardless of temp along with running issues if it were big enough to cause a no start.

EDIT: Missed that last part where you said you changed the FPR...