Hi guys... we purchased a commercial building and already moved a few walls and added a few electrical outlets... my question is NOW after we realized that we need the Certificate of Occupancy what is the best route to go for obtaining the right permits to get the CO? 

Don't forget the in progress inspections by Building and Safety, and get it final and Certificate of Occupancy when it is done.

Also, are you doing to provide tenants with the certificate of rent paid for the unit you are living in? 

If so have them both sign and file it now and when they pass you file an affidavit of death with a death certificate, and the property is yours.   

Unfortunately to close, the house needs a new roof ($1800) with certificate of no leaks and also a plumbing cert saying there’s no leaks.

The IRS has just issued updated guidance on OZ's including the draft self-certification form (Form 8996).

It's my understanding that if your property is pre-1978 and you're disturbing x sq ft of area (think it's 6 for interior or 20 for exterior), then you must be lead certified or use lead certified contractors if you're reselling or renting, may be exempt for owner-occupied, unless your state offers another option, like a lead-free certificate after professional testing. 

Look for licenses, insurance certificates etc. 

Property needs a ton of work and also lacks a certificate of occupancy.

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