If the bottom rot is only like an inch or so of the sill (bottom of window frame)
you might be able to cut it off and replace it. Clamp and glue replacement sill filler
strip on the bottom. Then screw them together as well. Don’t forget that the
bottom of the window frame sill has to be angled to fit the bottom of the sill frame,
so make it long enough to accommodate the angle. Counter sink the screws to
accommodate the fitting of the bottom angle so you don’t run your plane into a screw.
Yeah, it’s a bit of a pita, but easier than a total rebuild. Just a thought. You might be
able to do the same for rot on the sides if it’s not too rotted.
Oh yeah, mate the windows to the openings and mark both before you begin.
Sounds like you might have to rake out all the old caulking also. Darn, this is turning
into a real project.
I worked with my painter Dad for years. Guess who did all the caulk removal,etc!