i doubt they ever been off unless when it was a new boat.lol i had to take a very thin scraper and go all the way around the housing to bust the seal on it looked like it had some kinda silicone seal all way round.. pain in the ass regardless but had to be done..

Ive done two boats now.. its easy, but time consuming and dirty/itchy work..
You've already gone that far.. fix it now the right way..

ive done them as well on other boats im just gonna put glass and a tight fitting plug in it for this summer and redo it next winter ill have the engines out again then anyways...

If you dont have any rot down low I would not replace the whole transom. I would fill these spots with good solid wood, seal properly and enjoy. Just because you have rot around two bolt holes doesnt mean the whole transom is junk. Drill some test holes in other areas that are prone to rot and see what your results are. Replacing the whole transom is alot of work and money.

You need to do core samples of the stringers and engine mount pads the wood is a wick and will suck up all the water it gets If you have that much rot there more than likey the whole back of the boat is rotted out.

+1

I agree with the earlier post. Better do core samples all over and also check stringers/engine mounts. Been there, done that!

Drill out to solid wood with a LARGE bit, chisel the rest... then use "laminating & layup epoxy" & filler from "rotdoctor" (very flowable stuff)... follow their "routine", as long as the rot is not real extensive and you will be good as new. Their epoxy is different than any you have ever seen & it is not brittle like fiberglass resin is.