I can't speak directly to an '88, but I would think it might be similar to my '02, in that we don't have the "false" flat sole that is caulked in as the later boats do. Instead, at least on my boat, the cabin/cockpit bulkhead is fiberglass tabbed to the top of the cockpit "floor" which is also the upper skin of the actual hull. So no caulking is involved on mine.
If mine developed a leak there, therefore, what I would do to fix it on my boat would be to clean the area, sand/grind down to bare fiberglass, and then repair with biaxial fiberglass tape and epoxy resin. I would likely use the plain biax tape that does not have mat attached to it to reduce bulk, but as always, would have to decide for sure based on "being in there" and seeing it. I would not use any caulking at all.
Your boat may not be the same, but it seems it might be. If I come up with a photo of mine in that area, I'll come back and post it so we can compare/contrast.
Okay, here are a couple of photos. On my boat there is/was an installed drain right in the center/low point beneath the center of the cabin door. This simply connects the cabin to the cockpit when a plug is removed. The original one was a bit ugly and the fasteners were not the greatest, so I removed it and installed a new one. These photos were taken when it was out. So the "seam" you see just below the hole is the junction of the cabin/cockpit vertical bulkhead and the "sole" of the boat (which is the top skin of the actual hull).
The first photo is the cockpit side of it. The white stuff that looks a bit like caulk is a topically applied gelcoat to sort of hide the tabbing. The second photo is the cabin side. The bulkhead in this area was "hard" all the way through (i.e. all glass or gelcoat, no caulk or coring). Are yours similar? (You may not have that hole.)
