If you put 25% down when you purchased it, then you already have sufficient equity to do the rate/term refinance before you do all those upgrades.

Some other things I thought about was asking price, rents, rentability, ability to raise rents, will it cash flow after I move out and rent out both sides, age of roof and hvac, what kind of cosmetic upgrades would it need right away, are the current tenants paying rent and in good standing or should I ask for the duplex to be delivered empty at close, the leases of the current tenants and how long the leases are. 

You can't upgrade it (like with dual pane vinyl instead of single-pane wood sash) and a lot the stuff you need to pull permits for needs to get architectural OK. 

My wife and I are flexible in terms of exact location in Colorado, we are looking for a single family fixer upper to live in for 1 year before we upgrade.

I would try to pull whatever strings I could to get my deposit out, but if I couldn't do anything about it, then I would absolutely move forward and try to get as many upgrades out of the builder as possible.

., new kitchens and bathrooms, new flooring, removed the hallway carpet and installed an epoxy floor system - lots of fun and exciting upgrades!

., new kitchens and bathrooms, new flooring, removed the hallway carpet and installed an epoxy floor system - lots of fun and exciting upgrades!

Upgraded property with windows and heating system.

The tenants were supposed to move out as we were not renewing their leases and then we'd turn over the units with all new layouts and upgrades. 

@Joseph Cacciapaglia the cash out refi makes sense. 3 of the 4 units are going to need cosmetic upgrades in the next 7 years.