1.7 % of Loan Amount (Points) - $6,035underwriting fees - $1,400Are the above fees reasonable or not for refinancing a mortgage?

Your property is fairly destruction proof, costs near nothing to maintain, yet you can charge above market rents.If your property is nicer (class B) where the carpet alone might be $6k or more to replace when the tenant spills hair dye everywhere, you won't be as happy as in the situation above.  

For example, could I use my SDIRA to operate a management company that charges my holding LLCs a management fee?

Signing the lease demonstrates they agree to the terms and then you can hold them accountable.If you don't do this, then the person named on the lease and paying the rent could disappear and you would have no legal authority to charge the remaining three for unpaid rent.

The reality is the opposite - if it's not in writing then the PMC doesn't have to provide the service or can charge extra for it!

Prior to me putting 50% of the unit into a special needs trust for him I charged him rent.

The Midwest is probably your best bet for a number of reasons.

Partners are happy because I don't charge an exorbitant fee and do a much better job.

If you don't specify a charge in your listing, you can't collect it. 

My take on this is to underwrite purchases based on expected LTR rents (I like rentometer and the BP's own rental estimator), but start charging 1.5x that rent for your MTR.