Codes P0251, P0370 and P060 only sometimes on start up, clear, and runs fine

Question

1999 G3500 Express van 6.5 TD 240,000 miles with recently changed PMD relocated to front bumper. Crank sensor replace 2 years ago. Vacuum pump new and broken vacuum elbow to turbo wastegate replaced recently.
When I start it up and no codes are displayed, it runs really well.
And, as long as I keep it running, no codes appear.
But when I turn it off, and restart it, I frequently get P02251 Inj Pump Metering control failure, P0370 Timing ref signal hi and P0606 PCM processor fault. If I clear the codes prior to starting the van, about half the time, it fires right up and runs normal. The other half of the time, it takes a long time to start, the glow plug light does not come on, when it starts, it acts like it is loaded up and it runs poorly. It idles ok, but in 4th lock up, it chugs and bucks with the check engine light on. IF I stop on the side of the road, turn it off, clear the codes, it fires right up and runs normally and continues to run normally until the next time I turn it off and try to restart it.
I had been running biodiesel but switch back to pump diesel. Initially, it seemed ok but then started the same failures with the same error codes.
If I drive it with the scanner in my lap, no error codes develop. It only occurs on startup. If I check the codes immediatly after I turn the van off, there are no codes. If I try to restart it again, it triggers the 3 codes listed above.
Would a weak 2nd battery be a possible cause?