So to get rid of the conning tower glitch I had to carve a hole in the deck, simple enough now I know how to do it, problem it destroys the uv`s, obvious really with hindsight, so learn how to do uv`s, not hard really, just time consuming, and skull crushingly boring, then channel 2 uv`s, took a while to figure this out because .obj can only have 1 set of uv`s, then bake an AO map for the new uv`s, few false starts here but got there in the end.
result
such a lot of work for a hole, the good bit was having to rebuild the hull again, because deleting mesh subsets keeps giving me errors. and to top it all off I have not tried it in game yet, so it may not even sort out the glitch, but we live in hope.