when getting a quote, ask them whether that is for “retrofit” or “new construction” windows.
Retrofit windows cost slightly more because they are not taken off a shelf but ordered exactly to your dimension. Your old aluminum window actually stays in place – only the glass is removed. Then the new vinyl window is installed into the aluminum frame. The new window will only be as water-proof as the old window was. Some vinyl strips will cover up the fact that the old aluminum window is still in there.
“New construction” mostly uses standard windows e.g. 4’ x 3’ (a retrofit installation might be 46.75" x 34.25" for the same window)
Example: I replaced windows in an apartment (all of them). A given window measures (visible portion of the glass) 45.5" x 34". I go to Home Depot and order this window exactly in this size. No nail-fin, for retro-fit installation. It’s $230. I personally install it in about 30 minutes.
The alternative is to buy a 4’ x 3’ “new construction” window, with nail fins. That would cost only $160. But instead of 30 minutes it will take … hours. Stucco needs to be cut (in my case). Sheet rock and/ or wood trim needs to be removed inside. Rotten framing will be exposed. Framing may need to be repaired. New building paper needs to be installed, screw the new window in, “forti-flashing” strips in the correct order around all 4 sides… mix new stucco and put it on. 2nd coat. Paint the stucco. Inside repair sheetrock and/or wood trim, paint. Could easily be 5 hours.
Most of those companies that “replace all windows” for one fixed price will do a retrofit installation.
There is no way to estimate how many problems you find when you go the “new construction” route.
Retrofit may not be the best choice if you have no or small overhangs and get a lot of wind blowing rain against your house. I believe casement windows (the ones with the little crank on them to open it) cannot be done in retrofit, and neither can awning windows.
Likely the guy with the $40k+ quote has such specialty windows, thus requiring more labor.
If you just replace some slider or single hung window, the material is on average $200 (Jeldwen) to $400 (Andersen) plus an hour of labor. Anything above that is markup to cover warranty/ overhead/ profit.
I replaced last December six windows for ~$1300 … did it with a helper in an afternoon. Jeldwen, for an apartment. We had heavy rain since then… no complaints, knock on wood.