My concern is whether or not I am able to rent out a home after living in it for 2 years if I used the down payment assistance/ grant?

We will also be doing the LLC route my only concern is the lending portion. 

Why would someone leave a window open in 0 degree temps long enough to freeze pipes?

Lower your risk, leave something for your children.

But, the other layer to this is, does it even need to concern me?

The pantry is a cupboard on the reverse wall of the kitchen, so you have to leave the kitchen and walk into the hall to access it.If you are accessing the house from the actual front door, it's a pretty standard entry.

The previous owner passed away and we found out after we made an offer that there was going to be an issue in the courts concerning the estate and executor.

While I do understand your concerns about them not being on a lease, unless they are causing you problems I would not post a notice.

The smart lock allows me to assign codes for different tenants, remove codes when they leave, lock and unlock doors for repair people all without having to be there. 

However, this home is in Berkeley and I am concerned about destroying historical elements and potential added structural engineering costs that could make the house attractive to a buyer in future years, along with the opportunity cost of construction now versus getting rental income from the house in the next few months.