Try wiping the painting with a baby wipe. I wouldn’t want to use soap and water over the entire resin surface as I don’t know if any would permeate through/underneath and ruin the painting. Not likely, but not sure I would take that chance. Also if your resin isn’t completely cured, water will ruin it.
You can fill in the craters, but unfortunately, the surface won’t be level. You can try that first to make sure the silicone is trapped underneath, then once that resin is cured, cover the entire surface of the painting with another layer of resin. That will give you a smooth surface over the entire painting.