I just put down some Shaw resilient vinyl plank flooring in my rig. Like yours, it had some gross purple shag stuff in there before. I ended up having to rip out the entire plywood subfloor and replace it with some 3/4" treated plywood with a 1/4" lauan plywood underlayment over that before I felt comfortable putting down the vinyl. You can see some pics below. The second picture is actually the first in the series; you can see what awful shape my subfloor was in. That's after I removed the shower pan and the existing vinyl sheet.
People swear by Trafficmaster by Allure as well for flooring; I went with Shaw because...well, I don't really know. It's just what I picked up at the hardware store. Seems to work fine.
As for storage options, I'm planning on putting down the money for a SwingAway hitch
. I need all the storage I can get for rock and ice climbing gear inside the rig, and I'll need to store it under the bed in the back with a slide-out drawer, so it makes the most sense for me to be able to swing the hitch mounted box aside, open the door, and slide out my climbing gear drawer. Your needs may vary; the SwingAway is an expensive option.
Note when you're shopping for hitch-mounted stuff that a lot of what you'll see is designed and rated for power wheelchairs. Someone else may have more experience with that hardware, but my research indicates that it is not strong enough for the kind of storage you'll want mounted on your Class B.