Hi boatstalker - can you please post your model file? I can't really tell what is wrong just looking at a screenshot.

For 2 pieces to join, they have to be connected at a pretty tight tolerance - if there is too much space or a gap between 2 pieces they won't join. That might be what you are running into, but if you post your model file I can examine it more closely to check.

Is the scar you are talking about the line running down the deck? That looks like a surface edge. Most of the time if you join or union edges like that will remain in the final result, mostly the only exception is on some handling of planar surfaces where sometimes a union can combine 2 planar surfaces into one larger plane and remove interior edges.

- Michael