1. you would probably be okay with the weather stripping and only 1/4 inch gap. but
2. you could pane down the high spots with a good hand or draw plane.
3. take the boards apart. set up a table saw with the fence and rip a small portion off of one side of each board. then use this side and set the fence up again and rip the other sides to say 5 inch total (basically the 6" side is 5 1/2 inch wide and you are taking a 1/4 inch off each.) that way at least you are starting with boards that are exactly the same width. this will make it easier for you to make them even no matter if you butt them, dove tail, miter etc.