But to me it isn't obvious whether the existing appliances can be depreciated on my taxes since they weren't explicitly purchased (i.e. they weren't itemized on the purchase contract) by me when purchasing the bldg but they were included when I took ownership.And if the answer is yes the existing appliances can be depreciated then does that also apply to other non-appliance items such as the bldg roof or the 3 furnaces in the basement that are used by the first floor storefronts?

It has to be a strictly arm's length investment, and most self-directed IRA custodians will require that you hire an unrelated 3rd party property manager to ensure it stays this way.  

It's worth $130k and current notes are $125k.  1st loan is an ARM loan at $100k. 2nd loan is a balloon with 25k principal.  

there needs to be an arms length transaction, having the old owner might show signs of not obeying those rules,

To find out about an area go to IREM.org search for ARM certified property managers.

I say partially, because I also used personal savings I saved explicitly to buy property. 

Use arm's length lease-option documents along with the counsel of qualified professionals.

But whenever I hear "system," I get leary, especially if they're charging an arm and a leg for it.

I broke my arm snowboarding and it was sort of expensive.

Having said that, you may be able to twist the board or management's arm if they refuse to abide by the law so that off-site owners are included in the happenings of the association.