This time it is much easier since we submitted a play using the preset configuration from the city.

It is still an IRA, just configured differently to open up the possibility of investing in things always allowed per the tax code, but not sold by the big Wall St banks and brokerages.There are two plan formats you can choose.A self-directed IRA custodian (generally a trust company) can hold and report on the IRA much like a mainstream firm.  

Should I be worried about the zoning requirements for RH relative to the current configuration of the building?

Owner occupants started looking at duplexes and the occasional 3-4 unit depending on configuration driving those prices up to unreasonable levels. 

I have tried several tools and many configurations over the years. 

All your properties and all listing sites on a single configurable calendar, plus occupancy tax reports, automated rental agreement creation/mailing/archiving, travel and damage insurance for guests, quickbooks integration, door lock integration (not mine, unfortunately), email autoresponders, and more.

I have a distressed SFH under contract which is currently configured as a triplex, which the seller says was not ever approved by the city, and that I will need to apply for a variance from the city if I go through with the purchase and rehab.

I have acquired a property in the city of Tacoma which is configured as a duplex, but was never legally done so.  

Do I leave it this configuration or do I convert the upstairs into a master and one additional bedroom making the house a 5 bed 3.5 bath?

Depending on the size/configuration of the house, $10,000 isn't unreasonable (though you can probably get it done cheaper).Regardless, don't believe what you read on HUD PCR reports...they are meaningless.