powder coating lasts a long time and is cheap , not sure if you can do it on aluminium but its worth a phone call to find out .
shield city pc in staines are good pm me for the number if you want a price .
It may be worth having a look in pbo and scuttlebutt, as several posts on the subject over last 6 months. There was at least one thread, which commented on the fact that once corrosion has set in, recoating just highlights the defects
OK MB, now I can answer your question with more authority and to greater effect.
If you can get the windows out all the better, not only can you re-coat better, but rubbing down will be easier. If not mask the fibreglass around the window and the glass before you start.
If the finish has only partially gone then wire wool on the areas affected should do the trick and allow you to finish with a coating without too much work.
If not then wet and dry will have to be employed. Never use courser that 180 grade on any aluminium, the scratches will be a nightmare to get out. Start with a 600 grade wet and dry and a bucket of water. As you get rid of the damaged coating move to 800 or 1000 or even 1200, its all about feel and the effect you are having. Once you have got all the coating off and the aluminium is looking good, finish with wire wool.
The next stage is to decide what finish you require. If you want to paint them use a Zinc based primer, like the primers used for sterndrives. After all, they are made from aluminium and painted with a Zinc primer and an Acrylic top coat. If you want to go for a clear finish, say with a satin look, then don't polish the ali too much on the finish, then coat with a clear laquer. Anodising is better though, as this is chemically bonded the the metal, but I don't know any costs. I have achieved several refirbs over the years with these methods, one I am about to try is a clear Expoxy finish. Epoxy resins are used with great effect on wooden masts and hulls as well as on many areas in the marine industry that require maximum corrosion protection.
Personally, if you can find a colour that suits the boat, I would clean them off as described, Zinc primer, then use Acrylic paint to finish.
Thanks for the advise capn'jack I think I will go down the zink undercoat and acrylic paint route . Having replaced windows in the past I feel a satisfactory job (considering the age of the boat) will be obtained.