I do plan to switch to a pitched roof when the time comes where patching and painting out weighs the new roof configuration.

You definitely want to take a look at your debt and figure out if the return you would make on paying this off outweighs the return you would make on investing. 

The cons certainly outweigh the pros.  

The cons of keeping this tenant outweigh any pros.

Short term gain does not outweigh the long term risk.

But at some point the costs of all the LLC's and insurance will far outweigh the benefits as it eats into profits and complexity.

If qualitatively speaking you have concern and they outweigh the quantitative indicators (cash flow, equity, etc) then don't.

That's fine with me, because the benefit far outweighs the cost but keep that in mine. 

Does painting a 2 story cost more than a 1 story -yes- but does rents out weigh any additional costs because it is a 2 story? 

Seeing as most people looking on the MLS are working with a buyers agent I welcomed these agents in on the deal for 2% commission. 2% commission + $500 service fee outweighs giving up 4-5% commission on the sale of your home in my opinion.