Got the windows primed this afternoon.
I tried to get a closer look at the wood behind the weatherstripping. What I could see didn't look rotted. The metal weatherstripping has ridges in it and the wood behind is ridged to0. I still think I'll use the epoxy resin rot-fix stuff....just to be sure.
Sounds a good plan, easier (relatively) to do now, rather than later. Good luck with the epoxy.