Factor in carrying costs, then throw in some contingency, then a just in case fund, and pretty soon you'll convince yourself the bank couldn't give you the property for free! In my opinion if you get this property for $40K you should do that deal all day long.
I've been in this property twice. $16K Reno may be low, especially since the old oil boiler is a wildcard and paint and flooring through are a must. You may want to convert to gas for heating the 2nd floor and upgrade the electric to accommodate baseboard heat on the first floor since I'm assuming you'll hold this property long term so you'll want to make heat the tenants responsibility.
That being said, 90K ARV for a refi is also low in my opinion. You could probably refi for $100K down there, perhaps more with proper staging.
Why are your closing costs $9K? That's a whopping 25% of your offer! With a more realistic 4K closing costs, assuming you're using hard money at 3pts, that leaves 9-4= 5K for carrying costs carrying costs and the refi. The inspector may even let you rent out the first unit when it's done, cutting down on carrying costs.