In order to remove the roof cap on a '60-66 Chevy truck you will need to remove the factory seam sealer in the drip rail, around the perimeter of the roof. This will expose the factory spot-welds. With a nail set or center punch, hit every spot-weld, then you can drill out each spot-weld. I prefer a spot-weld cutter, because it only cuts through the top piece of sheetmetal, thus leaving a solid piece to weld to.
Once all of the spot-welds have been cut, the top can be removed. With a little coaxing, it will pull away from the adjacent sheetmetal. After removal, it will be obvious where the water penetration has occured. At this point, you can do the remedial work to allow the top cap to be replaced. Finally, make certain you install a suffucient amount of seal sealer, to ensure there is no further moisture penetration, at the drip rail. This area is a historical location for moisture weaping, so make sure you do what is necessary to avoid this in the future.