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.
https://www.amazon.com/dp/B001JSYH5G..._L0Fivb1B1JPCJ
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.