My total cost with holding and construction was $925,000 roughly and I am getting a loan to refinance my HML of $640,000.  

I would actually live here for a little bit, obviously not for years but its a decent little first apartment.

The previous owner got $1370/month total, I brought that up to $1600/month. 

RealtyTrac predictions), the residential properties are worth ~$3.5mm in total (give or take).

Basically a total renovation.  

The obvious......what permits are needed, what work has to be redone, how much opening up of walls/tearing out has to be done, the process, etc. 

Take a look at your financing package and understand what your total annual increase in net worth is.

The purpose of the Quit Claim deeds is to totally isolate the "company" assets for liability reasons, also so that the "company" is something I can sell one day to another investor, or give to my daughter by making her a member.

I purchased both for $308,000 total in Dec 2015.

If you own say, 10 rental properties, obviously you don't want to do that under your own name so people often create an LLC when they own more than 2 properties?