I'm in the process of diong mine right now but am doing it the way a friend just did his. His family also owns a paint store and I made sure that I am doing it the right way with the right stuff. I have a pro17 Tracker that was carpeted all over too.
I stripped the carpet, took out every part, drilled out rivets and re-did all those. I sanded the whole boat and took all the carpet glue off. I have the primer on the boat and as soon as this rain stops I'm gonna paint it and let it sit outside and dry.
I'm using a primer from Richards Paint that's just called Universal Primer. It's somewhat thick but is made for any type of metal is rust resistant, waterproof, and alkali and chemical resistant. It can be put on top of rust and still works. The paint my friend used and that I got is a two part paint. It's acrylic aliphatic polyurethane enamel and then you have a seperate bottle of the activator. It's a bulletproof tough paint that you can add nonslip stuff into it and mix any color you want. Problem is though if you wanna take it off sometime pressure washing won't even start to get it off. It's a little expensive but the best stuff for the job so you don't have to do it again a few years down the road.