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Do you have a way to test low fuel pressure? Can you by chance borrow a different scan tool to use?
I would test low system fuel pressure. It's possible your low pressure pump is failing over time. The FRP sensor can also be faulty and cause this issue. I would try bleeding it from the return line which is the rear line without the shrader valve
You shouldn't have to reset anything unless fuse 74 blew. It wouldn't run if this fuse was blown. With the rear line loose crank the engine over and will it start?
That is what I would do while bleeding the system. I always start the engine with the line loose.
The 6.4L is common rail. The injectors are fired by hi pressure fuel. They need 5000psi in order to fire the injectors. When the engine was newer it was common for the HPFP connectors to not fully seat and come loose again.
Disconnecting the battery and you don't have to reveled the system?
That almost sounds like a low fuel pump issue. It also could mean there is an issue with the FRP sensor. If you have a scan tool that can reset the high pressure fuel system you can see if it helps.
The shorting wire harness shouldn't be able to ruin a low pressure pump. The fuel pressure sensor you are correct. It should read .49-.50 with KOEO.
I don't blame you. I hate having to take this engine back apart after doing a lot of work.