The property looks like a duplex however it is technically considered to be a townhouse because each side is separately deeded.

Can i just include it into both rents and technically pay them myself?

So I'm not technically a newbie to Bigger Pockets (been following BP for about 6 months now), but I never did an introduction when I first joined and Bigger Pockets really helped me close on my first rental property about a month ago so I figured I'd go ahead and introduce myself. 

I have a goal of becoming a sophisticated investor one day.

Although you, a member, or even the sole member of the LLC will occupy a unit, legally speaking, an entity does not have a primary residence and also would not be approved under HUDs guidelines, so technically this may be a breach. 

MOST of the time they won't act on this, but technically they could.

I recently had new windows put in ($5900), will I be able to write them off on my taxes even though I'm not technically a business? 

The complexity limits you to only sophisticated investors, most of whom if they are investing in buy and hold would prefer a set it and forget it approach where the property just does its thing for 30 years until the mortgage is paid off.

It is very common for mortgage company to manage the claim funds over a certain dollar amount, as the property technically is their asset and the bank wants to ensure that the repairs are performed. 

Technically she has 157k in equity?