Scupper Tubes and motor well draining?

[rclauss22]

Alright Ive read all the threads on replacing the scupper tubes and transom tubes etc. Picked up a 1969 20 cc found in boat yard garage guy died years ago and this thing was left with running engine and new transom which was done in the 1980s sometime and used up until 2006 etc etc. Transom was replace but he never put back tubes in the holes that allow engine well to drain. Transom seems solid as a rock and the inside of holes are covered with whatever he painted boat with but you can look in and see the laminates of the plywood beginning to crack ever so slightly and i wanna stop it from doing anymore. My question is would you suggest drilling a larger hole trying to get as much of the wood out if water saturated and and filling with git-rot or epoxy then redrilling holes thru a solid epoxy barrier or just say f it and 5200 the hell out of it and stick new ones in? (as i said transom is solid i stood on lower unit at 225lbs and there was no flex at all). I also found the deck scuppers leaking a bit Ive seen threads where the scuppers once again where over drilled rotted wood taken out filled and redrilled. Just nervous about not drilling straight, drilling thru bottom of hull again etc. My question is which is easier this boat is what it is im trying to spend as little as possible. Expert advice?