While I know these numbers are not 100% accurate, I want to be consistent in the tracking method and use something that is simple (so I will actually do it every quarter).  

If you do something simple Security First title can record the mortgage terms for the owner -- I did that on one of my deals -- we spelled out the terms (interest and how id make payments and when they were due etc -- they recorded it for us)Wasnt super official - but worked and owner was fine with it.

Small, simple pitch roof could be anywhere from $4-8k, depending on several factors. 

I have realtors to contact if I'm looking for more property or need an opinion on comps.I keep most of the deposits with the same bank that holds the mortgages so very simple there to track money going in and out (I keep that separate from my personal banking of course). 

To keep things simple, I will ignore inflation, probable rent increases, and similar variables.

My concern is i may not be capturing all needed to give me the truest information. 

The simple fact that VA has a funding fee and conventional products don’t does not make it a more expensive loan.

Whether you pay interest on all of it or not must be negotiated.If this was a simple mistake on your lender’s part, per @Stephanie Medellin’s advice above, you should send it back.

So in the future you could refinance the rental to take out tax free money to pay down your primary residence to accelerate this even more, or sell the rental to capture the equity in it to pay down the primary residence.Regardless of your choice- refinancing would probably be in your best interest on one or both of the properties. 

It was not just a simple name change 5+ years ago.