Water...
Yeah, this is a common issue with this model and others. The construction of this boat has a molded "bilge pan" that is laid into the hull as a separate piece. It is only bonded in certain places. See the construction details in the owners manual. Because of the shape of the "pan", there is plenty of room for water to sit between the "pan" and the hull. You cannot see or gain access to these locations unless you drill holes through the "pan". You'd want to be very careful doing this for obvious reasons. The water will slowly migrate to the bilge sump (where the pump is) via weep holes as the boat heels back and forth or during any rocking motion. If you remove the small cover over the bilge sump, sponge out the water that's there and then watch while shifting your weight to get the boat rocking, you'll see the water running down into the sump from one side or the other.The most probable sources of water for these "hidden" areas are from the shower drain, the cooler drain, and if your engine bilge has been modified by drilling a hole in the lowest point (near the front of the engine). The latter is not recommended because the water can be contaminated with fuel and/or oil. Leaky hatches, ports, stancions, etc. could also be contributing factors. The plumbing diagram for this boat show the shower drain and cooler drain routed to the bilge sump via corrugated drain hose. I cannot see that in by 87' model. I believe those drain into the hidden areas instead.The soft wood sole you describe is a symptom of that water being there and soaking the underside. As you can see, the underside is not varnished or treated with anything from the factory. It's recommended that the bottom of the sole be treated with polyurathane or varnish to help protect it from the damaging moisture. However, in your case it may be too late. When I was in the market for a boat, most of the ones I looked at had soft soles. The one I ended up buying has a mint interior including a sole in perfect condition. I plan to put some water-proofing on the underside when I open it up again to explore solutions for this hidden water problem.Things to check for leaks: Thru-hulls, packing gland, keel bolts, raw-water hoses and strainer. If you're showering in the head, that would be a big contributor. If you use the cooler a lot, that'll put some water down there. You mentioned having to use a manual bilge pump,do you have an automatic electric pump? Does it run often?