Yes well, update. After having it back for more than a week, driving it everyday, I have had no problems with miscellaneous electrical problems. The clock/computer has not reset since I put the battery in. We are currently about 200 miles from Home, north (no camper or trailer). It gave me trouble on the trip up. I am still concerned about the secondary fuel pump, might just replace to be cautious. I haven’t let it get below 1/4 a tank since I got it back on the road.
I really wish there was a definite answer as to what solved the electrical issue, I might not ever know. (And I might not ever trust it).