Huh? Someone say cheesesteak??? I've been casually watching the thread, but didn't want to have too many cooks in the kitchen. But since someone promised cheesesteaks...
My thoughts are that you guys are getting out in the weeds with the stuff like leaking EGR valves, bent AFM vanes and brake booster issues*. Of course, all that stuff could need some attention too, but I think you need to focus here first:
The OP measured his fuel pressure and it was too high. Then he replaced his fuel pressure regulator with a brand new one and it was STILL too high. In fact, the new regulator behaved exactly like the old regulator. That's something that needs to be figured out first and it doesn't sound like it's the regulator.
The 40 psi too high with the pump running and the engine off could easily just be gauge error. I'm not too concerned about the difference between 40 and 36 with the engine off, but the second sentence...... "Fuel pressure while idling is 40 psi as well"? The engine will drown at that pressure.
So I would pose the question to the collective... Other than a problem with the regulator itself, what could cause the fuel pressure in the rail to be way too high while the engine is running? Return line plugged? Too much static pressure in the tank?
*About the weeds... The brakes feel pretty much normal, so there may be some leaking at the booster, but it's not catastrophic. The EGR valve might be stuck open a little and leaking some exhaust past, but that would cause it to run lean, not rich. The AFM vane bent a little wouldn't cause the FPR to be non-responsive. And the water temp switch... The engine is designed to run relatively well with the switch in either position. Just with lower emissions on one position or another depending on the temperature.