I recommend you do not touch the ways with Emory paper that is just asking for trouble. Take some scotch rite and wd40 and scrub till the majority of the rust is gone then wipe clean and hit it with a stone if there are high spots. Clean again then give it a coating of way oil.

For the paint I recommend ditching that coolant. I just got some QualiChem 251c in my machine and so far it’s awesome coolant. Does not affect the paint and no rust. Then continue cleaning the machine out and just resealing it don’t worry about the paint.

Im not sure if every Fadal leaks but when I get way too much coolant build up from tons of chips piling up mine leaks a little.