[dsraven]

from experience with my roof, it will be difficult to get the roof flat again because part of it is behind the inner roof so access is nil. you could try the unispotter idea if you have access to one. it may pull some of the low spots out. with a big panel it is harder because what you do at point A affects the roof at other points and can be a big "oil can" issue especially on a hot day. it would be best, obviously, to replace the darn thing but that is up to you. if you are just getting the truck good enough to drive around and not doing the rest of the body work then maybe just fill, smooth, prime and carry on, replace the roof later. remember since there is cutting and welding involved you really should gut the cab at that point when replacing so no pinholes in the upholstery or gage cluster, carpet etc. also, there will be some concern for the rest of the truck paint at that time. the cab would be a lot easier to work on if it is off the frame and lower to the ground. if doing later and removing the cab then there are all the other factors like hood alignment, fender alignment, wiring, etc etc.
sorry, my 2 cents is to do it now while it's apart. if it was some other small job maybe it makes sense to wait.
your truck, your wallet, you decide in the end. a full mud job may look ok and last for a long time too. I suggest to mud the complete roof after doing a few tests to ensure there is no oil can effect present first.