You may be correct about the ground loop but after trying two ground loop isolators and running dedicated peer and ground to both the HU and amp (experimenting, ran both components directly to the battery) without improvement, I decided to punt.
It was getting warmer so finally spent some time in the garage to finish sanding down the sub box. Added another layer of fiberglass and then it was bondo and spot filler. I was going to carpet the box but decided to paint/clear instead. Put some poly fill inside and it sounds great!