., but they will not file the approval certificate with the city after the work is done...  

The areas we are most confused about are the financing, and the logistics of doing this with the LLC while we live out of state (what addresses do we use, state tax, etc.).We have a decent understanding of how one buys a house and some of the regulatory stuff that comes with being a landlord (certificate of occupancy, etc.), but is there anything we should be especially aware of, or wary of?

BTW, FHA does not certify 203k contractors......the "certification" is from some private organization, that is not recognized, nor necessary.  

Find out if there are any down payment assistance programs that you qualify for, first time homebuyer programs, or if your state offers a Mortgage Credit Certificate ect. 

Or, do you need to go for NFI certification, National fireplace institute?

Instead of college go for certificates.

When they provide the receipt and "Lifetime Warranty" certificate they deliberately put a different house number on it.

In my area (Bay Area, CA) $5k doesn't buy much but it is plenty to become a well informed, well educated, and well certificated professional. 

Jake I'm assuming it's the certificate of occupancy.

Aloha,Your purchase agreement should be asking for copies of all rental related documents, PLUS an estoppel letter/certificate for any occupied units.