With respect to paying for expenses in connection with real estate owned by the IRA, not only do these expenses need to be paid with funds from the self-directed IRA,  existing assets that you personally own or through your business or a business of a disqualified party cannot be sold to the IRA to improve the property.

My wife and I are interested in buying commercial property in her home town. The specific property that we are looking at has a couple of retail store fronts along with 2 apartment units.What are the best things for u...

So, here is my question... how does the quit claim deed work with the existing mortgages (there is a first and second, totaling $118k)?

This is literally why they exist

You just have to make sure that you follow the rules/regulations and disclose everything that is necessary. 

Also good contractors virtually don’t exist in the fix and flip space so you need to be very diligent when selecting crews.

I still create spreadsheets elsewhere, but I'll track the existence of the spreadsheet in the software as a task so I can go to one place to know what I have.

Can't hurt to call/write a letter to some sort of ombudsman, regulator or the bank's customer service.. 

Even if the owner is willing to leave a key, what about liability issues for existing damages that could get blamed on you?

The problems already exist... so they would only be a new problem for the latest lender, not you.I would of course stay on top of this but I wouldn't let it ruin my refinance.