I brought my 2001 voyage up to New England from FLA in 2004. After the first winter it was obvious that I had Water penetration on the starboard rub rail which also acts as the joint for the deckhull seam. The Rail is H shaped and has a flange from both deck and hull interlocking into the top and bottom of the H. Spent 2 years drilling holes and injecting calking ( factory recommendation) as well as calking on outside slowed it down but problem continued. Finally Cut out rails and glassed over. The port rail was just starting to leak. If you have any unexplained rain water penetration look at your rails secondary damage is more expensive than rails repair.
While on hard disconnected bilge pumps for 2 weeks while we had 5 inches of rain. Not a drop came in. Before I would have been flooded.
We still love our 38 but this was very expensive. Jay
Unfortunately builders cut corners when they put the lid on the shoe box. Best method is, as you have done, glass the top and bottom together. Sorry you had to do it after the furniture was installed. No fun but you now have a much stronger and watertight boat.