Mine is also clocked lower on the passenger side. I have an automatic so it gives me better clearance to the pan. Not sure if they meant to do that but it works good for me. Could also be the 6 holes drilled in your rear mount are a bit off, making the mount not level when the transfer really is.
I store mine, headliner gone, too, outside up on milk crates and I have no problems. I think covering stuff can be worse than not, so I don't. I haven't seen any cause for concern in 3 years.
I even wash it once in a while--inside and out.
That's a th350 from a 4x4 set up. To get the t-case on it you need the adapter to go from th350 to either a np203 or np205 (different adapter.) I could sure use one of those short out put shaft jobbies, myself.