This home brings lots of character and tons of upgrades including: New HVAC, roof, energy efficient windows, flooring, bathrooms (with tasteful vanities and Italian plank tile), upgraded plumbing & electrical...etc.

I'd choose it based on which unit gets you the most rise in rent after upgrades, move into that one, fix it up, then rent it out (possibly to existing tenants who want to upgrade for higher rent), then repeat until all are upgraded, you've met your occupancy requirement, and then all can be rented at full market.    

I had a contractor look the property over already, the property needs approx. 25K repairs and upgrade, this includes the roof.

If the ARV is for the current layout of the property and you do the repairs/upgrades yourself, it may be worth spending some additional thinking on.

If you currently own another house that you are living in, maybe it would make sense to sell that house and use the proceeds to pay down the mortgage on the investment property to free up cash for the repairs and upgrades.

I will definitely be upgrading to pro BP.

What about telling the appraiser about the upgrades you've made, the scope and quality of the work that was done? 

Small upgrades can make the property more desirable but will it rent for more?

I think that's where I would start then if you end up doing more than 5 contracts/month you can upgrade when you have to.

They're growing in popularity for people who are environmentally conscious and it supports re-greening an area.