2 man crew. 10 hours to install 40 windows & 8 doors on 2 separate jobsites?

Did you account for set up?Staging? Did you really think you could go balls to walls for 10 hours a day 5 days a week?
It all depends on how much detail and workmanship you want to put into it. With your estimate, I'd say there is time for little or no quality.
I think 2 guys are doing great to install 20 some odd windows & 4 doors in a day and you want them to do that in a morning? Get real!!!!! You can't have ANY quality install doing it that fast!!!
It sounds like you underbid it.