All which can come off should come off. Some old plugs with a bit of grease on the threads and half way wound in works to plug those holes. I keep a collection of plastic plugs around for this kind of stuff... every plastic cover/plug/protector I ever see. Pull the dizzy, disconnect any lines/wires. BAG everything you can, tape all with masking tape.
You may have an issue with rust removal from the block if I interpreted your "brown" comment. Mineral spirits and paint brushes work well to clean grease off. For rusty cast iron, maybe the heat resistant POR? I never tried it, so no opinion. I've used Ospho and wire brushes in past. Did this B engine "in-situ" but it was painted well before assembly the last time I had it out, so no corrosion issues.