Instead, I'd like to enter into an option to purchase agreement with tenant, i.e. she pays me x dollars now for an option to buy expiring 6/30/22 for example.

There were and still are Millions of home owners under a forbearance agreement due to loss of jobs/income.

When purchasing under conventional guidelines you can supply a signed lease agreement.

The zone of the property requires approval of a special use permit to make the change.I've been reading up on the special use permit process in Stonington but the question I have is: Are we allowed to do the process prior to closing (with the seller's agreement, of course)?

Wondering if there was a structured way to make an agreement with a seller, hold it for 3-4 months during rehab after agreeing upon a price, offer some percentage above that based on sale as a carrot, maybe upside based on final price.

If the tenant is willing to allow the vendor in unsupervised, that's an agreement they can make themselves.I only escort the vendor if there's a legitimate reason to assist or if I want to use it as an opportunity to inspect.

I am 30 and have a high paying job and a decent amount of savings.We're trying to draft an operating agreement together as an LLC and I am trying to make sure my bases are covered.

That said, I would try to speak with the tenant first and get to an agreement before deducting or charge anything from their deposit. 

(Part of the sales agreement is that the seller has 4 months from closing to move out and she’s in the unit I will turn into 2 units and the garage that will eventually be storage of some sort).

What your Agreement says?