So after my last build got picked apart a bit I pulled the port out and sat down with the actual math instead of just winging it. Turns out my original tube was way off from what I thought it was tuned to. Once I accounted for the elbow bends adding effective length, I worked out what I needed to hit 36hz and cut a new piece of PVC to match.
The funny part is the box actually looks better now. I mocked up where the port sits on the top panel and drew out a couple alternate spots with a pencil before committing, ended up going with dead center so both subs share it evenly. Tested it tonight with a few bass-heavy tracks and it's a night and day difference from the old setup. No more that hollow one-note boom, the low end just rolls out smooth now and the subs seem way happier down low. Still need to seal up a couple spots and throw some carpet on it, but man, actually doing the homework instead of eyeballing it was the right call.