2009 Cummins ISX CM871 communication error? or not?

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2009 Kenworth W900L, 3 weeks ago just cruising down the road the truck stumbled, a quick intermittent power (electric?) loss, got to the shoulder and she just shut right off. Would crank but not fire up right after that. While sitting on the shoulder and turning the key most times there would be no lift pump sound. Fortunately only 40 miles from home so I towed it. Installed Cummins ReMan ECM, lost communication on first test drive, stalled out but fired back up. Got it back to the shop (experienced hands not a fly by night) and we then replaced both ECM wiring harnesses and the ignition switch. On Wednesday I took the truck on a 30 mile drive and had no issues. 2 hours later I go back and it was hard to start. Eventually fired up. Yesterday I wanted to take it on another test drive before I had planned on going back to work this week. I drove 27 miles, no issues, I get back, truck sits for 2 hours, go to start it up to put it away and it will crank but not fire. The ABS does it check but the lift pump made no noise. The only code that showed up on the dash was J1939?? At one point my ELD which always come on when the key is turned on did not come on which was a first. So after disconnecting the batteries for 5 minutes I turn the key, now the I hear the pump, she started, ran rough for a few minutes then smoothed out. I got her parked and continued to shut her down/start her up several times, no issues.
Once she started it would say No Faults Found. Batteries are 1 year old and all the connections were cleaned Thursday.

So what the heck can be causing something like this after changing what we changed? Could it possibly be my 7 year old Omnitracs power cord interrupting the system? Or something else on the truck we've overlooked?