We communicated every detail continuously, and even bought a dehumidifier to take care of moisture in the basement.  

They are quicker and moisture is not getting through an overlapped seam..not a chance.  

They use the cash flow from each property to pay for itself then the excess is used to pay themselves. 

Is there a water/moisture problem etc.... or do they just want cosmetic work done? 

If you used the FMV at the time of conversion to rental use to determine your depreciation, then you will also have excess depreciation to deal with which will be taxed as ordinary income.  

It would be easier and cleaner to just open a new IRA account with Schwab (or similar) and transfer excess funds/cash flow from your SDIRA custodian to the new IRA.  

Option 1: Do I take all of my excess cash flow (which I don't need) and pay down the debt as fast as possible - with the intention of refinancing, using the proceeds to purchase other income properties.Option 2: Save all of my cash flow to combine with my other savings to fund another down payment and just do this as quickly as possible (while still keeping a reserve for disaster etc..) 

Cash flow in excess of $200 per door and on track for a return in the neighborhood of ~10%.  

If you already have an ample reserve fund in place for the unexpected emergencies, then using all your excess cash flow to pay down the loan principle should be OK.  

That does seem excessive.