You're welcome!

For mixed breeds nest boxes... I'd suggest maybe 13" square since you have a BO, and you could put a one smaller on top of those bigger ones
for the little gal.... If the bantam is a good flyer put hers on top, she'll probably like that.... They like a little privacy too, so either make a cloth/burlap curtain or use wood to close the open in a little bit. Lots of good suggestions on this forum, you just have to figure out the right search terminology so you don't get too derailed off the main track......
Another trick I use is to google chicken nest boxes, (if that's what I'm researching) then select the images option at the top of the search page. This way you can scan hundreds easily and follow the link to the specific page for that style. Except Pinterest . I avoid those as they're too much work and it doesn't take you to the original posting, just to someone else's favorites list.
For ventilation I would cut two 12" or so squares out of each door (in front) near the base, or alternately on both sides near the doors, also as near the base as you can, and securely cover these with 1/2" hardware cloth. (Home Depot, lowes, Menards,etc) small rolls are easier to find. Then cut two long, but not too long rectangular openings on each side at the highest point you can manage. Something about 2-4" high and 5- 10" long would probably work. Again, make sure to cover these with 1/2" hardware cloth (1/4" is good too). You don't have to worry so much about covering these holes to make the coop warmer, (the birds can stand the cold) as getting a good air flow. What they mean by drafts are vents that are directly behind the birds when they're roosting that will blow cold air right on them, so try to balance the vents locations as best you can. The idea is to have the fresh air come in and flush out the stale out the top.
For the run, the best is to do all hardware cloth (1/2") but there again you have to research to find the best price in your area. I gave up trying to find what I wanted local because I wanted VINYL coated 1/2" in big rolls for my project, so I ended up buying from Academy Fence out of NJ. Cost was up there
Take some time to do some research on the different coops. I'm always looking at the coop section on BYC to get ideas. Also there are some great articles on ventilation if you just search BYC , several on sheds just like yours. Good luck! I'll try to check back when I can.....