If not do the boarding using the lag bolts to 2x4 on the interior VS using screws from the outside. 

You'll first need to hire an architect to design the unit.

No one is going to care that 3 people are in a bedroom "designed for 2 people".

Speak to the contractor's in-house architect and ask them what they need to see in the geo tech report in order to feel confident designing the house there.

Rethinking the design, the basement would likely also only have two bedrooms (perhaps each with their own bath for a higher rent) in order to accommodate the utilities.

I am an architect who uses generative design to streamline the production of mid-size projects but I am not a full-on programmer.

It is the policy design that matters.

The CapEx budget was $2.8M, or about $27,000 per unit, and involved complete gut renovations of 100% of the interiors and the office, as well as a total rethinking of the community areas and landscape. 

Assume the unreduced basis of the building is about $350k (I took out the land value)*Add New Deck - $8k*Interior/Exterior paint - $3k*Dishwasher - $500*Landscaping materials - $1500*Wood/sheetrock to build walls to enclose an existing space - $500*Furniture (beds, tables, chairs etc) - $5k*Hot Tub - $5kCan we use the SHST or De Minimis or Routine Maintenance safe harbor for any of this? 

Home office deduction is available if you have a rental property and designated space exclusively used for rental property business.