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No. It doesn't start no matter what we do.Throwing the idea out there. Cant you start the engine without the MAF sensor plugged in?
You said changing the pump made pressure worse so I would look at the pump. Maybe you have a bad connector for the spill valve. If you put 12 volts to the spill valve the pump should build max pressure try starting your car that way. Now what I would do next is Flash an off-the-shelf map with the correct maf cal to eliminate the tune as a problem. It will probably run like shit and I wouldn't drive with the map but it will let you know if it is keeping the car from turning over.
Now if you have air fuel and Spark the only other thing that could be stopping the car from running would be your ignition timing. That's based off your cam and crank sensor. If you have an AP just pull up RPM while you're cranking and see if it moves. You should also be able to monitor the cam sensor by looking at VVT since I believe it is based off the difference between the two sensors on the AP display.
Posted this in chat, but have you flashed a zeroed out map in R4 to both MAP A/B on the split second controller? Have you also configured the correct settings in R4? Have you verified that the MAF V and RPMs are reading correctly on the SS controller? Verify that the crank position sensor is on the right way. My dumb ass had it on backwards and had a similar problem. I'd eliminate all of the extra fueling stuff to verify whether that's part of it or not. you won't need it until you're under load anyways.
Oh shit!
Do MS3s break clutch pedal assemblies like MS6s do when you go to a stronger clutch?