i would do the frame rail first.
if your going to do extensions, and trunk pans, invest in a cleco kit.
http://www.lowbucktools.com/clecos.htmlthis way you can place, and remove panels as you weld, replace them.
whatever body you have left , providing it still is showing body line, will remain.
do the 1/4s next, roof lays on top of the c pillars.
you can skin the doors last.
theres lots of posts on panel replacement here, just use the search function. and im sure im the first of many who will chime in.
look here, its not as in depth as id like it to be, but you will see what i mean about clecos.
hope it helps. and good luck.
http://usera.imagecave.com/Obituaries/challenger/