All this reminds me of the circles I went in with my build. Seal up everything, fill with foam or leave holes for inspection, knowing water might get in?
In the end I went with enough foam to float the boat no matter what and limbers with inspection/ventilation holes. I have tucked all the inspection openings away from where most water will get in, and all the openings are in places where water would not usually sit.
If that boat was mine I'd reseal the bungs and be done with it. Remove bungs, look for any evidence of wet wood, dry well and reinstall and reseal. I'd epoxy the bung hole and screw holes as well.
If I had any doubts about water getting in unseen I'd cut out an inspection hole in the sole near the back, seal the edges with epoxy and put in an inspection port. This could be as simple as a clear perspex square screwed into place and sealed with marine gasket sealant. Removal may not ever be required, but you will have peace of mind.
I'd not muck around with pumps in that space.