It's technically an investment home as my dad lives in it and pays the LLC rent.

When I refinance (or technically purchase) the property down the line, is there a financing route that minimizes those downpayment costs?

I mean technically you can put whatever you want on the MLS listing, but if there is a discrepancy between the number on the MLS listing and the tax record then the selling agent SHOULD notice this and question you on it.

I would research Grand Rapids too, its becoming quite the technical center of Michigan.

You are at risk of becoming the "stuckee" (a technical legal term for getting screwed by city). 

In applying the 2% rule to the 3 units the deal works great, however, since I am planning on also making this my primary residence and covering the mortgage from the two tenants technically I would not be paying myself rent.

A Wholesaler technically has no oversight and nothing to lose in terms of licensing if they disregard the best interests of any or all parties.

You are technically killing two birds with one stone by checking on the property, tenants and also collecting rents.

We take over the property on a Subject2, season the tenant, then technically you could Lease option it out (their new loan pays off the old one).  

To be clear, I am condoning the search and exploitation of LEGAL loopholes to stay technically compliant while still serving your needs.