Welcome to JA! Do you have a Cummings or pacar software so we can do some testing?
what lead up to the batterys exploding?
If you have the scan tool for the engine lets do a system test to see what is or is not working.
if we don't have the tool to do this, lets see where we have power to
i would start at the run relay and go out we need to see where the power stops at.
That would have been the next step if we don't have a electronic problom then we need to look at the mechanical end .
i would also check and see that none of the broken check valve went into the engine, this would be past the fuel filter and little to stop any extra parts.
Ill be on and off here threw out the day