I had some leakage into the fore and aft sections on my Shearwater Sectional at first (thankfully not in the cockpit). To fix it you need to make sure that you sand the bulkheads are flat as you possibly can. The vinyl membrane alone can't create a watertight seal if it is not on a flat surface. Pay special attention to the areas right around to bolt holes. You may need to add some wood-dust epoxy in rough areas. Sanding and more sanding. And more sea trials.

You'll get there but it took me several attempts. Of course, you also want to tighten the bolts as much as you can so make sure they are very securely glued into the wing nuts.

It's a great boat and the sectional structure makes SUV transport easy, but you have to pay a price in elbow grease.   

   Looping back to this issue.  After a lot of sanding and analysis, I'm pretty sure that some of the t-nuts that the big bolts screw into are slightly out of true, so that even when I tighten everything down as much as possible, there is a gap between the gasket and the wood that lets water in.

Any advice on how to fix this?  I can't think of a way to remove the t-nuts to try again that wouldn't do far more damage.  Should I try redrilling the holes on the hatch side so they align better to the (out of true) nuts on the cockpit side?  Would a thicker and squishier gasket help?  If so, what material would be best for squishing and keeping water out?

thanks!

I'd look for some kind of silicone material you could fashion your own 'custom' gaskets out of, one or two layers of something around 0.063" / 1/16"?

How thick depends a lot on what kind of gap there is between bulkheads when sections are bolted together. Maybe use two gaskets on each bolt, one larger than the other rather than both being the same size?

This kind of thing is pretty easy to find as a baking accessory, used for rolling dough out onto.

Another possibility would be a simple neoprene o-ring of the right thickness & diameter. There are also flat "fender" washers in several sizes in hardware store selections, ID small enough to fit tightly around bolt but wider than a typical washer, of neoprene rubber 1/16" thick. Neoprene's not as 'squishy' as silicone though, so may need some trial-and-error before you have to resort to doing anything more permanent.

I'm not entirely sure I understand what you mean by saying that the T-nuts are out of true and thus causing the problem. The male side (the T-bolt itself) is free and can be moved around quite a bit to ensure alignment as the hull is bolted together. The female side (the nut for the T-bolt) is set firmly in epoxy. It that was not seated properly before epoxying it in place, it could create a tilt as the T-bolt is treaded into the nut. The result of a tilted bolt (a couple of tilted bolts) could make it impossible exert flat, level pressure as the bolts are tightened. And that could cause leakage even if the hull sections are level.

Before doing anything, I would try sprinkling both sides or your vinyl gasget with chalk dust (or something similar). Assemble the boat. Test it briefly in the water. Disassemble and see if you can diagnose the nature of the leak by examining the washed out pattern in the chalk dust.

But if the nuts for the T-bolts are not set in the epoxy properly, I suppose you should heat them up to soften the epoxy, knock them free, and start over in reinstalling them according to the initial manual instructions.