I am no expert but here goes
1. Sounds normal
2. Chalking is normal oxidation if it is a rubber roof. I would only clean twice a year and no treatment. I cleaned and treated with Protect All and my roof was showing black and had to be coated in 8 years, I think the treating may have accelerated the aging. It sure didn't help.
3. Needs to be addressed as soon as possible. It will not go away. I would take something like a screw driver handle and tap the floor to see if it is rotted or just a normal sub structure issue. Normal should give you a sharp solid sound and a good bounce. If rotted it will be a soft thud. Find the leak and fix it. Remove and replace rotted wood or coat with "git rot" if still somewhat solid. Dry rot doesn't need much of a moisture content to continue to spread. Search "fleetwood wheel well" on this site if you want see my little floor project. It can be done just takes a lot of labor.
