I know the roost bar needs to be above the egg box, however does it need to clear the top of the egg box?
In your design I see that your nest boxes are going to be pretty much on floor level. I would place a board across the front, to keep most of the floor litter from being scratched into the nests. Keeping 4 chickens, I don't think a secluded nest-box is all that necessary. I would simply place nesting material into one corner of area . and leave it open. With 4 chickens, I guess all will be happy using one nest (same), even if you make multiples.
Going to put a window covered in hardware cloth below the vents but don’t want it to be at a level to be too breezy with the roosting chickens...suggestions on how far up to put the roost bar and windows (and how big should windows be)? Both sides will mirror each other...total of two windows and two vents.
Make window opening whatever size fits construction well. I would also have a closable,, outside,, framed Clear Plexiglas window that you would close during cold weather. You still would have daylight entering coop year-round. In summer, keep opened and hardware cloth (installed on inside wall) would provide predator protection. Do same on both sides. In summertime hot, the breeze will be welcome for the chickens. In winter, the roosting chickens will not be affected by closed windows. You still have the round vents in place, and those need to stay open year-round. The ridge vent also helpful for ventilation.

So place your roost where practical, and you can always change height/location as you see chickens using it.
There are numerous ways to install those windows. Use your way, or ask and I can give you option in how. (hinged,, slide-out,, screwed on for the season

)
Your coop looks deluxe.

WISHING YOU BEST,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,and,