Joe,
With the old top removed and before installing the new top, I had removed my top frame for painting although ended up powder coating it. Upon reinstallation of the frame, I moved the frame back while the 3 bolts and nuts on each side were still loose. Although there is not a lot of adjustment there, it helped align those wood strips. My observation was that they were either out of alignment by about the 1/2 inch you mention or in alignment, sort popping into place. It is difficult to get to those bolts with the rear interior panels in place. I will try to post a picture of the new top, but the one I just tried had to large a file.