Hey I know this is an old post, but can you share what challenge it presents if the bolts break? I want to soak mine in a good break free product but in the event that I break one head off, what will I need to do?No real need to remove the upper-side panel.
However, if you are replacing your roof for rust-issues, then likely you should also take a peek at the seam between the upper panel and the lower cab rear/sides. The gasketing there, as well as the weatherstripping between the roof and the side panels, is often cracked, deteriorated, or missing after so many years. Water finds its way into those areas and then does its magic.
Watch when winding-off the roof bolts--too often they are so rusted they simply twist off--replacement with stainless bolts and anti-seize works better for future dismantling. And if your pickup truck is pre early 1970s, the mid-cab j-hooks are prone to breaking when re- latching the upper backside to the lower cab. The hooks are made of cheap pot-metal and can't take the cinching over fresh gasketing unless everything lines up perfectly. Nothing overly dramatic, just as always be prepared for something to snap or something to need replacement when you thought you'd be done quickly and back on your way.........just my two cents, anyway.