Start with the simple stuff before ripping out fuel pumps, injectors, etc.
Limited should be relatively easy to remove and check.
I'd try something like the Moly fuel system cleaner first.
Disconnect the fuel lines and stick them in the container and do a few cycles of cranking the juice through the fuel system. Let it soak a bit and then repeat.
If some contamination is causing your problem, this may help.
Just checked further back. You've checked the SCV valves, but did you checked if any voltage appears at the plug?
From what I understand about the common rail systems, there's always some fuel bleeding back to the tank, it's part of the cooling strategy for the injectors.
The output of the high pressure pump is totally controlled by how much juice the SCV let's into it.
I would have thought an injector stuck open would let some fuel into a cylinder resulting in combustion of some sort.
Life was much simpler back in the carby days.