My question is, when you raise the top there seems to be a gap between the back window on the sides and the top , leaving it open to the elements. Is there something I'm not getting or is there some adjustment that needs to be done.

 

There should be no gap open to the elements. Something is amiss.

Do you have the factory service manual? You need one. Better yet would be to have the body manual, which more likely would cover the top.