We have a 5 unit property in Willimantic , CT. 

The stays at your property are mid-term, but for repeat business, you want to cultivate long-term relationships.It sounds like you are well on your way to doing that.

The type of loan on your current property is largely irrelevant. 

My question is - Bracebridge is experiencing issues for long term rentals for people looking to rent a 2 or 3 bedroom unit, and these are very scarce as prices to own escalate and property management for long term rentals is scarce also.

I'm looking for properties close to where I live in southern PA so I can manage my own properties to maximize cash flow.

My advice is to buy good properties in good locations even if you have to forgo cash flow.  

Obviously, I don't want my properties making people sick.

I know some regular conventional investment property loan programs have certain rules about this but does Fannie Mae?

We use it for managing our portfolio of SFRs and small multi's and it handles everything accounting wise for the properties so there's no need for quickbooks.You can also run your property management business expenses through Buildium or use Quickbooks if that's easier. 

I did a HELOC on my primary property to buy this one, which I rent and the cash flow is good.