What specifically in the rear is not lining up when you have the front lined up? Is it at the drop offs? The tail light panel? The back edge of the wheelhouse? A picture or two might help quite a bit if you can manage some.
You don't really have much you can play with in the front, but all the sheet metal you replaced in the rear would effect how the rear lines up. If one or more of those pieces aren't meeting the rear of the quarter panel, you may have to do some surgery back there. BUT it all depends on where the quarter panel is not meeting up. In some cases it's just a little bit of creative clamping and wacking.
1966 Mustang Convertible - T Code - vintage burgundy / black pony interior
1966 Mustang Coupe - C Code - currently red / black standard interior (going back to original dark moss green / ivy gold and white pony interior)