You are getting a lot of conflicting information, which is perfectly normal. Everyone has their own opinion on what magic numbers work best. We are each so unique in climate, set-up, management techniques, goals, flock make-up, experiences, and everything else that there is no magic square feet number that works for all of us. If you have roosters, let broody hens raise chicks with the flock, or integrate new chickens into your flock the space requirements jump. If they are all mature hens you don’t need as much space. If they are confined to the coop a lot you need more room than if they have access to the outside. You’ve indicated you will roof and block off your run to give them outside room in the winter. That helps a lot. Chickens don’t understand the concept that this is the coop and this is the run. They consider room to be room, wherever it is, as long as it is available. If you wish, you can follow the link in my signature to get a bit of discussion on this.
It’s not a point that at some magic square foot the situation changes from everything is absolutely horrible to everything is paradise. It’s a gradual change. In general I find that the tighter I pack them the more likely I am to have behavioral problems, the harder I have to work, and the less flexibility I have to deal with problems. Commercial operations have shown that you can keep certain chickens, all hens the same age that have been specially bred to take confinement well, in as little as 2 square feet with no outside space at all. I’m not going to work that hard or micromanage them the way I’d have to so that can work. I’ve never heard of anyone complaining about having too much room once it is built (it can get expensive) but many complain about having too little.
From what I know about your situation, I suggest you make the run as large as you reasonably can. Rig up at least some of it next to the building to keep snow out (snow can blow in from the side) and create an area where they can get out of the wind. This cul-de-sac doesn’t have to be huge, the main thing is that it is outside the coop so they can get separation if they need it. One way chickens have learned to live together as a flock is that when there is conflict the weaker runs away or just avoids the bully to start with. It’s not a matter of square feet, it’s a matter of getting away or avoiding. Quality of room counts.
Most building materials come in dimensions of 4’ or 8’ standard sizes. At least these are typically the cheaper dimensions. If you are buying new material and base your design on these dimensions you can normally build it with less cutting and waste plus maximize your space for the money and work. Why do you think that deck is 16’ x 16’?
You have a lot of options. As a minimum I’d split it down the middle, half coop and half storage. That’s probably the simplest cleanest way to go. 8’ x 16’ is a lot of storage. You do not want that to become junk storage. Mice will be drawn to the coop by the chicken feed. Don’t give them a cluttered area to build nests. Easier said than done, I have that problem. A major clean-up is required here, but I digress.
Make the coop high enough that you can walk in without banging your head. Slope the roof or use gutters and downspouts so rainwater runs away from the coop and run, not into them. You don’t want rainwater hitting your head when you are opening a door so watch door placement. When you design your roof, have a decent overhang so you can leave the top of the walls open (covered with hardware cloth or some type of soffit vents) for ventilation without letting rainwater in.
Chickens create a lot of dust. They shed dander, create dust by scratching dirt or bedding, and they scratch their dried poop. If you have openings into your storeroom, dust will get in there. Depending on what you store in there, you might not want that but you probably want a door to the coop without going outside for convenience of feeding them. On the other hand, if that storeroom has decent ventilation, like the area under the overhang, it gives you the opportunity to increase your ventilation without worrying about wind or rain. Trade-offs, trade-offs.
At some point you will need to clean out your coop. If you make your run gate and run-to-coop door big enough to get a wheelbarrow through or at least shovel through you may be happier at some later date.
You’ll get a whole lot of conflicting opinions on windows too. I’ll give you mine. Some people like a bright coop, I don’t. I like it to be a little darker because I think they are calmer when it’s not too bright. You and they need enough light to get around in there without electricity so you do need a window or two. Also, it needs to be light enough in there so they can see to go to bed when it gets dark. If it is too dark in there when it is just starting to get dark outside they can’t see to go to bed. If you have a security light you probably don’t want that shining through a window. They do need dark downtime. I don’t know the exact size but I have one regular surplus house window on the north wall and it works in my 8’ x 12’ coop. If you go 8’ x 16’ you may want to consider two. Windows come in all shapes and sizes too. You can use anything from a framed hole in a wall covered with Plexiglas to practically any window you have or can get from the store or maybe a habitat recycling store if you have one of those around.
In all this think about your convenience. Giving them more room so you have fewer problems to deal with, more flexibility in dealing with problems, and you have to work less hard is more for you than the chickens. They can get by with less space but it’s harder on you. Having convenient access in feeding them instead of having to traipse outside though even more snow is for you. Make chicken keeping relaxing and enjoyable for you, not a source of stress.
That’s enough rambling. You have a great opportunity there. Good luck and welcome to the adventure.
