David, I still can't get over all the work you did with the rig standing, great job.
There are a couple of things to look for regarding the bad core. The most dangerous is the loss of the inner skins at the bevel. Wet core around the stantion bases really weakens the laminates inside and out. The worst damage seems to be where the bulk of the crew sits when on the rail. Getting off the rail, the stantions are torqued hard. In the case of my (late) 25 deck, I was able to pull the midship stantions all the way to the cabin, with little effort. The inside skins were fine though, but the rotted core had weakened the laminate so much it was totally flexible. On Ursa Minor it was different, the inner skin had broken at the bevel. This means the inner skin is no longer doing it's job, the problems too many to list.
On GFornal's boat, I chose to tape the hull and deck, waxed the surface and layed up knees in place. When cured they were removed and cleaned up a bit before stantion installation. This method allowed the knees to be removed for any reason, including rebedding he flange. Made certain the knees were large enough to act as backing plates for the stantions. Ursa Minor need the added strength of the knees bonded to the hull, so I glassed them in place. That was much easier but the option to rebed the flange is challenged a bit.
Really inspect that bevel fore and aft, look for the tell tale black mold. A simple fix and not a bad idea at all if you can, glass a tape or two over that bevel, it can only help. I would also suggest using vinylester resin, not epoxy for that fix, I kinda think thermal expansion is more important in that area than the use of epoxy, plus the vinylester can be gelcoated easier. The epoxy/carbon traveller beam on GF's 25 was gelcoated, but the process is a pain, wipe with water is all it takes for midcoat adhesion. ( I do NOT suggest anyone do this)