Since bedroom sq footage is cheap, we have increased the size of the units by adding the space to the bedrooms.  

Software does OK with objective data (SF, bedrooms, lot size, etc.) but fails with subjective data like photos (condition), proximity to nuisances, etc.Below is a summary of the comp selection guidelines we follow.Distance: All comps should be within 1 mile of the subject if it is in an urban or suburban neighborhood.Age: All comps should be within ten years (newer or older) of the subject property.Size/square Footage: Only above-ground square footage is calculated in the square footage.

Do I use the comps from homes with equal square footage, bedrooms, etc. to arrive at comps? 

I was told by the commercial lender I was using that they would not finance that property either because the square footage of the commercial/business part does not meet their requirement (ratio).I'm going to have to ask her to clarify and tell me who would be able to finance if they can't.

@Fang Underhill most lenders have square footage requirements.

West side of the valley, rents vary based on sq footage (gross leases)

What you really need is footage of you flying the drone, showing what you can do.

Just the practicality of the property like if the basement is finished , square footage, and how many bed/baths there are compared to other properties.

A better layout, more open space, more square footage, extra baths, etc will lead to better quality tenants and larger upsides for rent.

In addition to renovating the whole house, we added square footage by removing an atrium and changing a work space in the garage to an enclosed laundry room.