I use (and have had good luck thus far with) Dicor Self-Leveling Lap Compound, applied over the old after cleaning thoroughly. Dicor Non-Sag Lap Compound is a different product for non-horizontal applications.
x2 on the MaxxAir or similar vent covers. The ability to have the vents open in the rain is priceless, as is the ability to have them open while en route. They also help keep pine needles and leaves out of the vents (although imperfectly).
The air conditioner is generally not installed using any lap sealant or other caulking; instead, there's a rubber gasket between the air conditioner base and the roof that keeps everything watertight. It's not a bad idea to occasionally remove the interior trim panel from the ceiling of the motorhome and snug the air conditioner mounting bolts a bit. They don't need to be torqued down very much, just snug.