When I got my Space Mission (and also any other older game) I thought about what it would take to keep it looking good. Then I thought about clear coating, touch ups etc. I wound up just doing a few touch ups and cleaning and waxing it. I stopped obsessing about it and decided that the enemy of good is better.
If any inserts have sunken I would definitely fix those. Clean it, get it running and then deal with the cosmetics! Good luck!