I think your first step, if you haven't done so already, is to apply for a mortgage to see where you stand.

Business license or other 3rd party proof that the business still exists as of when you apply for the mortgage (CPAs don't write these letters, these days). 

It's feeling near impossible to find funding as nearly all of the lenders I've called either require you to be local to apply or the deal has to be over $x million. 

Warning: this exception applies to corporations only.

Then applied for reciprocity in CT.

Would me having one already close to maxed out be a red flag to lenders if I were to apply for one on another property?

Also, that may not apply to rehab.

do tenants get an exception when they apply for the occupancy permit?

JT,(A) One accessory dwelling unit and one junior accessory dwelling unit per lot with a proposed or existing single-family dwelling if all of the following apply:(i) The accessory dwelling unit or junior accessory dwelling unit is within the proposed space of a single-family dwelling or existing space of a single-family dwelling or accessory structure and may include an expansion of not more than 150 square feet beyond the same physical dimensions as the existing accessory structure.

However, every lender I’ve applied with so far won’t do a loan amount over $780k (which I thought was odd as I would have expected any such cap to be $765k, the conforming loan limit in this area).Do you have experience doing a jumbo cash out refi?