I opted to just epoxy + fiberglass over those holes, I made an extensive post about the process here
. Long story short, just use two part epoxy for the small ones, with a thickening agent if necessary (or a penny!), and for the larger holes, like those for the lights on the sides, use cloth or even better spare sheet metal that hopefully you saved from the demolition. I've abused the epoxy/fiberglass combo for everything on the bus--if it's leaking, or needs a stronger seal, or I suspect it looks a little flimsy--I'll just reinforce it with fiberglass. There's better and prettier ways to do it for sure.