I have a double window that has a rotted windowsill. I am have to replace the whole thing because there is so much rot. I was wondering if there were any secrets to doing this. Both windows are double-hung. Any help will sure be appreciated.
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Well, as with just the sill, you need to fix the original cause of the rot, either first or at the same time the window is replaced.
How you go about replacing the window depends a lot on the sort of siding you have, what kind of exterior trim is used, etc. It also depends on whether the window (presumably old) happens to be a currently-available standard size.
First step is to remove the inside trim and get the rough opening measurement, and also measure the window itself, the exterior trim, etc.
Then see if you can find a standard window to fit.
A certain amount of difference in windows (perhaps a half-inch of height and an inch of width) can be compensated for in the exterior trim, if you're not really, really picky about appearance.
If a standard window won't fit (it helps if you can actually put a tape measure to the window, vs relying on specified "rough opening" sizes), you can order either a custom-sized "standard" window or a "replacement" window. There are some who would argue that you should order a "replacement" window in any case, as it will be better designed for replacement situations, and because you can get it built to a more precise size. But with most standard windows you can remove the exterior trim and nailing flange (though be sure to check!) and have the equivalent of a replacement window for what is often a substantially reduced price.
If I were doing a one-off replacement, I'd remove the old window, including trim, do whatever repairs are needed to the opening, then remove the trim from the new window and (tentatively) install it "bare". You can temporarily attach scrap strips in place of the trim to help align the window. Once you have the window positioned the way you like it, fasten it more securely, rip the exterior trim to fit, and install it. Be sure to put Z flashing above the top trim, and do whatever sealing and caulking is consistent with the type of siding, etc.