I assume you took more pictures than the ones in your dropbox archive?
Regarding the windows, that’s what I would do, though I’m not the expert on architectural stuff (waiting for Götz here):
I wouldn’t mask them.
After reconstruction I’d probably cut the distorted reconstructed glass planes and add new 1-polygon planes in. Assuming they’re all on roughly the same axis, maybe 1 plane would be enough per floor.
Next up Retopo, then reproject texture and maybe paint the glass planes a single color, or add fake reflections.