Quarter Fitment Problem

The gap in the corner is supposed to be there for water to drain out, from what I can see they fit pretty good. You can use a block of wood and a fairly large hammer to convince the trunk floor extention into place. Then use a set of C-clamp type vise-grips to hold it place while you weld it up.
Just remember that these things were mass producced and were FAR from perfect from the factory. The big picture here is make it fit but don't allter the outer skin, if you do all you've done is create more wor for yourself in the end.

Hope this helps. It was really hard to see what you're seeing from the pictures, but anyway good luck and keep us posted.