I couldn't get your pictures to come up. But...
You describe scratches over most of the starboard side of varying depth. And you have paint over gelcoat? I'd say DON"T try to sand out scratches that are into the gelcoat, if that means sanding in a localized area, as you'll lose fairness in your topsides. They'll end up looking lumpy. Getting fairness back is a beast. Avoid. I see a lot of sanding in your future, but the sanding needs to be equal and minimal over the entire surface. Of both sides of your boat.
Any deeper scratches should be filled with thickened epoxy, and then sanded flush with the surrounding area.
If it was my boat, I'd resign myself to applying a two-part epoxy paint, and proceeding accordingly with regard to the best procedures for the product you've chosen. Sanding, priming, and so on.
I don't know your familiarity with two-part coatings...they can be sprayed by a pro or they can be "rolled and tipped".
The bad news is that you have a lot of scratches and a fair amount of work ahead of you. Just be glad it's topsides and not decks. The good news is that your topsides are going to come out looking great so long as you put effort into the prep and you're not a klutz when you apply the paint. Stay away from dark colors. Roll and tip can look damn good, but dark colors will bring out the flaws inherent with that method.
