There are epoxy/resin products available to treat small areas of wood rot. Because they are trapped in the window frame, sashs tend to have more extensive rot than these are meant to handle. If it is more than 2-3 inches, or involves a joint, you may have to have the sash rebuilt.

The big thing with older wood windows is getting them properly reglazed, good write-up here. http://www.rd.com/how-to-glaze-singl...icle45866.html If you have a lot of windows, many painters will do this for a fee (and listening to their sales pitch for a full house painting).

Is your house multi-story? If it is, changing full screens for full storms is a major spring and fall project. It also means you have to store all of the out of season storm/screens. That is best done by hanging them vertically, which takes up a lot of space. There is a reason combination storm windows became popular. If you have a single story house with easy access to the windows from outside, and the storage space, you might see if you can find some used storms and screens that fit at an architectural recycler. Then you could go directly to painting them and installing.