Okay....explains that as well.
So new VCT solenoids did nothing. With random misfires on both banks common sense says it has to be something in common with the whole system. So to review from memory, you've replaced the PCM with no change in symptom. You've verified the alternator is good and putting out proper voltage with no minimal AC ripple. Plus you just upgraded the fuel rails which had no effect. What I can't remember is if your fuel system is open or closed. If closed there is the possibility of a flaky FRP sensor. Otherwise since the PCM has been ruled out, the Alternator has (according to your voltage check readings) been ruled out, the only other thing I can think of in common with the system that could cause random misfires would be something in the fuel delivery system. Finally there is the fuel itself to question (but I assume you have tested it) or possibly the tune has gotten corrupted on the tuner (but I would assume you have reflashed the tune to the hand held and then reflashed the PCM several times. A failure on the PCM relay would cause the car to die as it provides 12vdc to the COP's. A failure of the Fuel Pump Relay would also cause the car to die (or not start) as it provides 12vdc to the FI's AND Fuel pump/FPDM. I would be curious to know if you have good 12vdc at the injectors with key on engine off however. PIN2 on any FI would be where you could back probe to see if you have solid 12vdc. It could be that the FUEL PUMP RELAY, though working has built up carbon on the face of the contacts which could cause a weak signal to the FI's which could cause the misfire.......BUT I AM REALLY REACHING HERE. I still believe there is something going on in the fuel delivery system. Vacuum leaks you would see on your vac/boost gauge and likely hear from a higher idle and lower boost.
Hope you get this thing figured out man. I know its a tough one. I don't envy you a bit.