Hello there fellow Floridian. I think the hardware cloth on the bottom & sides are a great idea. I burried 1/4" hardware cloth under my coop for predator protection too. For roofing I used 1/4" plywood, roofing paper & then shingles over that. Also don't forget the drip edge. I was originally going to use the plastic corrugated roof, but the shingles were stronger and a lot cheaper. They're a bit more work to put on, but you'll do it once and know that you have a steong heavy roof. With the heat and sun we get here in FL, I don't feel the need for transparent panels.
Post some pics of your progress. I still need to post some updated pics of mine, but you can lok at my coop to see what I did.
I am going to call it the Backwards Coop because we built the very secure run FIRST and then we "inserted" the coop using the existing walls of the run. That way, even if the girls are "out" of the coop at night, I have no worries. 
