Sounds like you have a lot going on.
I agree with the advice posted above to load-test both batteries individually.
Low battery voltage at startup can cause many different codes and symptoms.
Just looking at the three codes that you were currently concerned about, they could be tuning-related.
See the attached information on those codes.
As you know, the U010E code is for the DEF System, which should already be tuned out.
The P0607 code may also be tuning related to the injector “on” time.
If the U0001 code is an active stored code, it may be a CAN BUS C issue.
I realize we have only just scratched the surface so far.
You are on the right track to start with battery condition and voltage.
Then, look for some new tuning.
Please keep us posted and let us know if you need similar information on other codes that are not resolved as you continue to troubleshoot.
We are here to help as best we can.
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