I undertook a pretty thorough cosmetic rehab of the property, which included new floors on the main level; fresh paint on all walls, trim, windows, and doors; new countertop and sink in kitchen; new stainless steel appliances; new tub and surround and painted/updated bathroom; and epoxy paint to floor of basement.

I’m running into and issue, during inspection we found some water damage to a portion of the subfloor and joist under the kitchen sink.

If you look at this guy's kitchen, while it's nasty in terms of filth, he doesn't have wasted perishable food just strewn around.

In the design phase, I’m intentionally wanting to add features and value to later use as part of my long term funding strategy.

There are a few things I'd touch out (bathroom/kitchen) but they are minor things (again, this is something I will double, triple, and check again during due diligence). 

I contemplated the idea of just changing the design concept to have it be attached to the main home, but even in that scenario, the explicit CCR's against even renting one room seemed too controlling to be sane, considering that if this worked as we wanted, there were like 200 other nearly identical situations with lots with homes in that neighborhood that we would have just wanted to rinse and repeat that strategy.

If I could see a 200-300 dollar increase in monthly rent I would go for it but that would mean expensive upgrades to bathrooms and kitchens and I don't think the increased rent would be worth the expenditure-but I have not ruled it out.

First you’ll need an engineering design.  

New roof, installed central a/c, new kitchen, opened garage back up, new fixtures, paint, etc.

Accounting, Risk Mitigation, Marketing, Advertising, Branding, Web Design... you get the picture.A lot of those things can be outsourced but you still need to know enough about them to make hiring and project management decisions.If you're entrepreneurial and a confident salesman (or quick study) then I'd say absolutely consider it.