Get the A/C off the roof, place a heat pump twinned to the furnace, so they share the under floor ductwork. Roof insulation and penetration is improved, lower center of gravity, aerodynamics, over all lower height, a dual compressor system each wired to 1 leg of 120v so it would engage the second compressor if needed when connected to 240v.
Vinyl window frames, not aluminum. Again less cunductive of heat or cold, non corrosive.
Keep the rubber roof! I've had 4 aluminum roofs. Noisy, Dented, leaky at joints, electrolytic corrosion eats them up.