Kevin:
I've never pulled window frames on a C-Dory, but have removed hatches from other boats, which are pretty much the same thing. The biggest problem is that after you remove all retaining screws, the frame is still locked in place by adhesives. What you want to avoid at all costs is to remove the frame, and have chunks of fiberglass and gel coat come with it. That turns a fairly inexpensive project into something else altogether.
The only way I've seem frames removed without this additional damage is to tape the adjoining fiberglass areas, and then work a piano wire between the frame and the gel coat, all the way around, to cut the adhesive loose. You'll need several different lenghts of wire, each with a broomstick at the ends so you have something to pull against.
Once you've made the cut, you can work the frame loose with other tools, as long as you're careful not to bend anything.
There are also several products available which would work on the seal chemically. Check with West Marine.
Once the frame is out, a first class job would require that you pull the glass, have the frames sand blasted, etched, and powder coated. You then have to reinstall or replace the glass, and put everything back together again. This is a big project. If you do the painting yourself, it's still a big project.
Quite frankly, if it were my boat, I'd probably mask everything off, clean up the frame as best I could with sandpaper, spray on a little primer, and then paint with Interlux Brightside single part urethane. If you etch the aluminum before priming, the job will last a lot longer.
If they clean up fairly easily, I'd probably just prime and paint. If I had to spend a lot of time getting them clean, I'd etch, prime and paint. The bottom line is that if you don't properly etch aluminum, an oxide will form before you can get the primer on (no matter how fast you work), and the job will ultimately fail. But, if doing it all over again in a few years won't be that big of a deal, just prime and paint.
Let us know what you end up doing.
