Your heir will inherit the property and receive a step-up in basis equal to the market value at the date of your death.

We were exploring taking out a primary mortgage on their home to take out 350k in cash at about a 6% interest rate, and I take out a loan from them at an equal rate or slightly higher (maybe 6.5%).

Again the US Economy is remaining quite resilient.All things being equal, this would be good.

In scenario B, my offer is equal.

Ok, appraisers aren't perfect or created equal.

As for your "better off in the stock market" comment, your analysis is flawed because it is based on an equal cash vs cash assumption.

. ($400k new building minus $50k taken already equals $350k)

My father wants to use his SDIRA to provide a loan to the LLC him and I are equal partners in.The loan would provide the additional funds we require to purchase an investment property.The LLC would pay principle and interest at market rate to the SDIRA.Would this be considered a disqualified transaction? 

They always have the winning bid until the bid equals or exceeds the debt associated with the property.

The PM company charges a fee equal to first months rent for this lease only service.