Re: flat roof idea, built up oak floor without insulation
Replacing the windows would be a 50+ year payback in energy savings. Better to consider repairing the window seals on the existing casment windows. You can also fit Low-E storm panels on them to reduce heat gain.
I don't know much about roofs. The membranes seem to be a good choice and can usually add insulation after tearing off the old ones.
Not sure about the floors. So they are mounted directly on the slab? For a warm climate, that shouldn't be much of an issue. Your heating season is so short.
When you replace your heat pump, be sure to get it sized correctly. A oversized unit can use more energy than a proper sized on... especially in a humid climate.
1925 Two-Story Stucco Beaux Arts Neoclassical