Get your foot in the door and aim for a break even (if it means you can get started). 

Do not calculate them per square foot as every renovation is different.

Check the comps for sale prices by square foot. 1666 sqft sales for 419k for example  Residential build cost and commercial build cost are different.

If not then where do we start to get our foot in the door. 

Leasing at $3k/month covers your current mortgage comfortably, so refinancing could relieve the pressure of the balloon payment.

Until I get my footing and confidence in the whole deal.

Carpets in bedrooms are okay since there will be less foot traffic with shoes on in those rooms.

One foot in residential and the other in CRE. 

If the cabinets are touching the floor, I'd say put the cabinets in first and this way you know exactly where you need cut the flooring to ensure a 1/4inch gap between the lvp and the foot of the cabinet. 

If he were an adult, perpetrating a crime on a child under 12, I wouldn't touch it with a 10-foot pole.