Say What? ::
If you're saying what I think you're saying, then yeah, unfortunately it sounds like the frame-rails are in wrong::, and/or were put in when the car body was twisted. This is just my guess based on what you said. More details, such as how & in what order you replaced the framerails and rockers would probably help you to get a better answer from a knowledeable VMF'er.
Carefully trim the trunk lid at an angle, trimming off 1 1/2". Next owner will not notice for a couple months, and then WHOA "Look what the PO did!" and we all will layugh and say "do a search on trimming a trunk lid" Ha Ha