Also rims were previously glued and most spoke holes had been filled with a clear silicone type substance (to ensure they are sealed?). What can I use to fill the holes? I cleaned the rim surfaces and now they are clear but also stripped out theat silicone type stuff.
No need to fill any holes.
But if you must, there are mini corks made specifically for the job. I think they are silly, but if it floats your boat, by all means, knock yourself out.