From a purchase and tax standpoint, I would operate the business expenses as usual in the name of the LLC as previously done.

The extra cash would go into that reserve..Good luck.

Our renter stayed an extra year.

There are investors who offer them but they usually oly offer 60-65% LTV/CLTV plus it required No income - just rents.

You can see the effect on your equity position is of simply making the monthly mortgage payment using the rent payments.As others have said, there is no benefit to accelerating the pay down by adding extra payments no matter where they come from.Most RE investors will execute a cash out refinance at regular intervals to ensure that the equity stays in an acceptable range rather than growing too large.

Not a red flag, usually this means the owner didn't have the property for very long, or are just lazy.I would try to squeeze the agent to ask if the seller can provide a list of improvements made on the property over their ownership if any.

For entity type they usually have more importance

At best it will be based on 80, usually less.

It really comes down to whether the extra time for me to do it will cost more in lost rent than hiring it out.  

As someone else pointed out, the goal of a refinance after renovating a property is to get out your down payment as well as some extra due to the increase in assessed value.