1) Cosmetic issue with planets reloading their graphics. Most planets higher than 25 have ocean useable tiles anyway.
2) Why do you have them on both? it's a waste of a planet by capitalising both, but meh. No, I don't think you can rebuild starbases. Reload a save before you did it, else get rid of those Industrial sectors and replace with stock markets.
3) They don't count empire wide anyway, so that isn't an issue. Yes, they all work.