Drywall – What’s the best way/tool to cut a strip of drywall out of the window boxes

Single glazing with storm windows absorbs sound reasonably well, I would not expect a huge decrease in sound level with triple glazing, but certainly not an increase. Single glazing alone is another story, it's sound absorption is terrible.

The increased sound is certainly due to the frames and adjacent construction. While there is often a correlation between thermal loss and sound transmission, sound is much trickier to manage well. It is sometimes counter intuitive. The construction joints must be carefully detailed. The general concept is to avoid any solid connection between inner and outer surfaces. Any connections should be via resilient, absorbent materials. Typically, you want to fill any voids with sound insulation, though in some cases this has been worse than a simple air gap.

Also consider exterior sound attenuators. Walls, fences, trellises, large shrubs, trees, berms all will help attenuate sound, but when you consider cost vs. benefits, such measures need to be carefully considered.

Just get replacement windows instead of new construction and use tapcons to fasten the windows through the sides. Caulk outside good to keep out water. Foundation should also be graded away from the window to keep out water.