All great ideas Bobby. OP should implement all.
This post just goes to show what a mess you can get into down the digital rabbit hole. The faults being heard are almost certainly due to digital issues and like most here I would exonerate the amp. But adding a digital equaliser won't solve the problem. It's sending a spider to catch a fly. Just adds to the mess.
Like Bobby says clean up the whole system and simplify. Where possible put individual components in other systems to verify they operate correctly.