Should the body be bolted back on the fraame before removing and replacing the 1/4 panels and trunk pan?
thanks

Rob, Yes it is better to do the work with the body back on the frame. That way everything will line up correctly. If I had to do it all again I would have done all my body work first and then take the body off and complete my frame.
Ray

on my 69 GTO i had the body on a rotisserie and it turned out great and made replacing the entire floor (from trunk to cowl) so much easier than on the car. for the 1/4 panels i would do it back on the car that way the body is "resting" on the car and the lines will stay the same versus replacing the 1/4's while body is off the frame and the body may have flexed while off the frame.

Thanks thats what I needed to know

i am doing my trunk floor with my body suspended by the pinch welds on a lift. will do the quarters with it back on the frame

The body flexes many different ways, especially when the quarters are cut out because the car body can lose it's strength. On the frame and on tires.