I have yet to have a new build ever be done on time (which leads to problems moving out / renters moving in, and expensive interest rate locks extensions), 7 times out of 8 it ends up costing a couple points more than expected, so yeah, building a house isn't the coolest way I would try house hacking.As a side note, I've had an accessory apartment. 

Make sure your agent is on top of any extension request necessary to complete the deal.

Therefore, we had to move in a rental house and pay for storage for 3 months, on top of getting an extension on our loan, as well as increasing the amount we borrowed.

Based on your posting the damage seems to be extensive, especially since it’s affecting the structure of the home such as a floor beam, sill plate and subfloors.It appears there is active termites as well as a beetle issue and both must be resolved before repairs can de done.You didn’t mention home value, just purchase price so it’s difficult to say what to do from this point.At a minimum, I would have the termites and beetles dealt with and get a bond from the termite company to cover the first year for more treatment.Also, have a licensed contractor give you a repair estimate.

* Are there any more extensive calculators/spreadsheets for managing income flow around all of this and comparing against the opportunity cost elsewhere (e.g. stocks)?

But I am new to RE investing, so I don't have extensive knowledge in looking for deals.

I would like to work with a realtor that has extensive experience with the nuances of investment real estate and is very knowledgeable about the area in Bergen County (Hackensack, Tenafly, Fort Lee, Teaneck, Lodi, Leonia, etc.).

Additional increases will be required if extensive repairs are required by the Health Department.

For good tenants I sign an extension for a certain time period.

I've seen the house now, and it requires very extensive work to repair and update the property.