Over in the plastic airplane world a lot of guys favor working pure epoxy back and forth across the surface with a squeegee, removing all possible excess while wet. The idea is to fill the pinholes, not just bridge them so that they sand open again later.
I've done a little of that and it seems to work well. This time I'm gonnna try wiping with System Three ClearCoat, a pure epoxy with the viscosity of water. Started using it as a soak-in coating when building wood biplane wings and really like it. I suspect it will make a great pinhole filler on glass cowls.
After sanding it will get the usual (your favorite brand here) primer filler.