I would install the roll up after. If you have the c channel trim for he door opening, this will need to be under the door track. Also you want all the tweaking and squaring to be done before trying to adjust the tracks.
Pay close attention to the details of the trim that goes above the window and doors, it'll be all the difference of water leaks or not. It's not a big deal, just look over the details on your plans, I wish the guy that put mine up did.
Looking good, I'll be watching. I like the layout you have, especially the lean to being designed into the building.
Craig