I'm not sure on the specifics of the VA loan program but this question might be better directed to other lenders in your area.  

The landlord specifically says:"I want to you to know that I needed to use some of your security deposit money to fix the floors.

This is a very specific local question. 

Definitely sit down with your CPA to discuss your specifics- but above is a fairly common guideline

You can move another way and actually start an LLC for an EIN number, but you should consult an attorney for more about that in your specific state. 

What are the specifics on this to avoid capital gains tax in this situation?  

I did look up the local laws on rent increases but did not find anything specifically stating that rent could not be increased to market rates if a new tenant is placed.  

I already know the taxes for both properties and I have called the utility companies to get a round about number for utilities, but I wasn't sure if there is a specific document that may give me a comprehensive overview of the profits and losses for the current owner. 

If it's turnkeys specifically you are interested in, check out-https://www.biggerpockets.com/renewsblog/2015/12/2...With that said, right now I'm working with turnkeys in Indy, KC, Chicago, Philly and Baltimore. 

Are you looking specifically for a property manager in that area or are you looking for general management advice?