I'd just slather some more bondo over it, sand everything down and spray paint it. Not worth going to the trouble of replacing a roof on an old Jeep.

 

Someone tried that already, now look how it turned out

 

^This, at the very least strip off all the old Bondo and throw some good rust inhibitor paint on it. Bondo is not water-proof (regular Bondo anyhow) and it will continue to rust under the bondo if not treated, not to mention that putting more Bondo on top of the old stuff that is cracking/pealing would be a complete waste of time and would likely last a couple months at most.


Holes should be patched with metal (ideally welded, though body epoxy or rivets and seam sealer are better than just Bondoing over the holes.


If you don use any Bondo use Bondo-Glass, this is fiber-glass and resin based and is water-proof (though you should still paint it). It can't be sanded as smooth as regular Bondo, though on top of being water-proof it is much stronger and more flexible so it tends to hold up much better. Note: fillers of all types are meant to smooth the surface, not to fill holes or large dents and should only be used in thin layers.