In regards to the fish wear, Bay Area Amusements sells a decal for each of the fish. I have also seen a single decal that does all four fish at once but couldn't find it with a quick google search.
I always use an airbrush and Createx acrylic paint for touch-ups. Harbor Freight sells one for about $10 that may not be the best, but is adequate. You will need to clear or put mylar over any paint work.
Typically you want to re-paint the entire area until you get to a break (like a black line) since it's extremely difficult to exactly match paint.
If you're new at restoration I would do the decals on the fish and throw some mylar on the other spots so they don't wear any more and forget about them since they're not really that bad. In all cases level the inserts first (see Vid's guide for a complete playfield restoration).
https://pinside.com/pinball/forum/topic/vids-guide-to-ultimate-playfield-restoration