Hi Arnie. I went back and looked at the other thread you started, and also took a look at the instruction sheets online, as I don't have a set.
Your attempts at closing the gap are not the right way to solve this. Because you are right- your wood overlay will be the same size as the plastic part and the problem will reappear. The problem most likely started on the gun deck. You really need to take the upper deck back off now and go back down below and fix the issue. Otherwise it will keep reappearing- the transom wont fit, the holes for the masts won't line up, and so forth.
I am not sure what the problem stems from, but I have an idea. The gun deck sits on a series of ledges, but it also slips in under a series of little nubby pins that hold it flat and tight down on those ledges. In your pictures in your ROP thread you can see those pins. You can see that the gap is there on the port side as well.I think what has happened is that the extra thickness of the wood overlay has kept the deck from fitting in under the pins- they are jammed against the side of the deck rather than fitting over it.
You've also done a great job of building up the bulkheads, but it looks like there's enough clearance under the extra thickness for the deck to fit. So take the deck back off and look in there. It may turn out to be as simple as just clipping off those pins, but you'll need to get at the base of them or it won't solve the problem. The other possibility is to carve a little of the deck away from where they need to go. Either way I think it will solve the issue. But no half measures. You only want to take that upper deck off once, so be sure you get the thing all the way together before you leave it.
I hope that does it, good luck, and it's a fine looking model.