If you feel comfortable floating that with "Bondo", you might want to consider using polyester resin and micro-balloons instead. You can mix the resin then add the fine powder micro-balloons to a little thinner consistency and float it on with a paddle. Once it starts to cure, file of the high spots with a ShurForm flat file (at a 45* angle) just enough to remove the high spots. Then fill the low spots and sand again.
https://www.amazon.com/TILER-Surform...NsaWNrPXRydWU=
I once had to do that to the deck of my 45' yacht. It took me all day so you should be able to do that roof in half a day.
As for the vents..... just remove all the old calk and recalk with Dicor self-leveling sealant.
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1