I am also a Snapper owner .. I have an older 1995 model. At one time, I thought I was having a similar problem with the rubber disc being too close to the engine disc and the guy at the repair place told me that you can adjust the height of the engine disc by adjusting some allen screws that hold it on. Sorry I don't know the details of it because it turns out my problem was related to the transmission so I never actually adjusted the disc.
As for the axle boots, you will need to first take off the wheels by sliding off the hub cap and removing the bolt that holds the wheel to the axle. Once this is off, you need to remove the remove the plate that mounts to the mower body. There are a lot of bolts that hold this on. On one side of the mower, the transmission is mounted to this plate so care will need to be taken when removing it. More than likely you will need to open the transmission case when reinstalling everything so that you make sure you get everything aligned properly in the transmission. You will probably lose some transmission grease in the process, so it might be a good idea to buy a bottle upfront. Also make sure you create a good seal when bolting the transmission back together with a liquid gasket-maker (like that blue stuff you use for create gaskets in car repair).
Once you have these plates off, you should have access to the axle and be able to slide the boots on. You will need to clamp these boots on both ends to create a seal. I don't know if the clamps come with the boot, but if not you could use any standard screw-type pipe clamps.
I can't remember every nut and bolt I had to remove when I was working on my transmission, so some of it might be feeling as you go but I hope this gives you a little direction.