Retrofit Foam is expensive for sure. Using foam in new construction is definitely something to consider. Some of the DIY foam sites now tout a 1" foam application int he studs to seal for air -infiltration with batts installed behind to raise overall u-value. This makes a lot of sense to me...
Amerimax Windows out of Colorado makes a very good quality vinyl window. Their website is amerimaxwindows dot com. I had their windows in 2 of my houses and they were tight and operated well.
The do make windows with flanges. They are typically used in new construction though. You may be...
Many times the manufacturer will have their name stamped on the bottom corner of the glass if it is a tempered unit or their will be an ID code or name stamp on the IG spacer bar. I Have seen this type of damage very often on Pella clad windows. You do not mention if these are clad windows or...