Hi Brent,
You can remove the body and work on the BUT like other have said, be sure to weld in a few cross braces. I'd run one across under the dash one in each door opening and above the back seat. This will keep the body true and stiff alowing you to cut off the old rails and instal new ones when your ready.
You can either wait to line things up when the pan is finished or replace them while the body is off. If your not replacing the heater channels there should not be any problems with alignment as they go off the heater channel holes. Just be sure if you are replacing the pans to line them up to the heater channel holes first.
Geoff.
