C of O is issued by building department certifying that it’s up to code and you or your tenants can live in.

The number is: (2o2) 765-I264 and the attendee code is 522409519#Best of luck!!!

I know that banks will not lend if the property is not "habitable" (e.g. electrical, plumbing, etc.) but will they not lend if there are certain items on the CO report that have not been fixed during a refinance (e.g. window needs to be replaced, interconnected smoke detectors, fire code items, etc.)?

Find out the code words in your area.Good Luck and Good Investing! 

So long as you keep the house code violation free and put a $300,000 liability rider on your basic fire policy you'll have adequate protection.

I've talked to a few architects and dug through the code a bit myself but can't find anybody that really deals with this type of issue as it seems very niche and specific to three-families.

Additionally, the roof replacement is definitely the time to add insulation, and adding enough to meet local building codes is just as easy as having less, assuming a tear-off. 

I would suggest zip codes 33607, 33614, 33616, 33609 and 33611.

Probably too late at this point regardless, but there will likely be building code issues brought up (fire exits, clearance heights, non-permitted improvements).  

Have them put an electronic lockbox on the unit with temporary access codes.