My marker lights looked like crap too, but mine was several years older than yours. I found some at a truck stop that fit and where LED and I put them in with stainless steel screws. They've been in about 18 months now and still look good. I used plenty of silicone behind them. I concentrated on sealing the holes behind them rather than calking around them. So the silicone is hidden.
My roof vents also looked like crap. The covers are easy to do. But mine had this tiny little weak fan in them. So I took the opportunity to replace the whole unit them with fantastic vents. Covered one over the bathroom, since you need to open that one a lot, even in the rain. And I really like the see-through tinted covers. Nice to be able to look up there and see the weather.
Doing the whole unit it's probably 25 screws per unit and you need a tube of dicor self leveling lap sealant for each one you do. No worry about damaging the roof it's tough fiberglass. And you'll be covering with a whole mess is dicor when you're done.
Good projects if you're the DIY type.