Hey Grant,
Great space you have there!
I'll chime in some canadian two cents worth:
I would patch the existing roof with some filler/sealer for sure. Fill the cracks.
I'd scrap your idea about a deck; too many liabilities and too much cost imo.
Try building some removable 8'x8' cedar slat flooring panels; something like this pic:
You can build the panels with a very low profile, they can be built on some wide sleepers which will still allow for drainage below and load spreading over the existing roofing. You'll want to avoid any kind of point loading. This will also benefit the existing roof because the most damage to a roof is from the sun, so this can act as a ballast and protect the membrane, extending its life considerably.
I would spend some money on lighting, it will enhance the area for evening use. Forget the solar stuff and do it right.
I'd clean things up as much as possible; painting the doors, trims, etc. It looks like you may have a plumbing vent stack coming up behind one of the pyramid skylights; you should extend that up about 9 feet; it probably emits sewer gas smells? not pleasant for a deck? Probably against code too?
Measure everything to the inch and draw it all out. When you hire a contractor get referrences and give them the plans. Show exactly how you want things done. The cedar look is awesome for decks; so do the floor, add some planters, built in benching, maybe some columns/posts for lighting, hanging baskets?
Then you'll have some money left over too.
Hope this helps?