C of O

I would work with a mortgage broker on this. Universal Mortgage has done well by me. Adam Dahill, who posts here, gets good recommendations. Another broker/lender you can try is Frank Tamayo, ftamayo@metlife.com 212-413-4548. Apparently Met Life, sitting on the huge war chest after selling Stuy Town at the top of the market is lending at good rates.

Owner occupied/owner work could be good, could be bad. Unfortunately I don't think that pulling a permit guarantees a quality job. Lots of permited jobs cut corners, so you have to trust that the finishes will reflect the overall quality of work and that your inspector will pick up any red flags. I think that the biggest hassle is going to be that you will have trouble financing.

This shouldn't be hard, you need to verify that which zone is this and if it allows the use first. But are you sure you need a new C of O? What does the current C of O say? Assuming you are getting a new C of O. To comply with building code, there will be some work you need to do such as sprinkler, egress... and I can't answer that without seeing the space. Sometimes it makes sense just build partial hight walls to separate the space and rent it out by desk. But again,it depends on it's current condition and many other factors. And it is not legal to rent it out before you get the new C of O.

Many houses built before a certain year (I beleive 1938) do not have a C of O.