Hi eb,
I usually use silicone plugs to fit into the holes and silicone caps to fit over studs. They come in all shapes and sizes. They also make different types of high temp tape for masking. I also prefer if the part comes already stripped. It takes the guess work out of what could be under the current coating or if repairs are needed. If it still needs a detailed cleaning I prefer blasting with glass bead media for the cleanest finish.

Mark