If you take over the company that has good cashflow that's a good indicator but it would be good to vet those properties out by making sure they have the appropriate permits to operate legally. 

I have some work needing done that requires permits and the contractors aren't licensed in the city where the permit is needed.

What can we do, I am currently in a contract with this property, it is originally a single-family home and the owner added (3) 1 bed 1bath units at the back (without securing permits).

Assuming I had the experience, I would only buy a place with structural issues if I had 1) an experienced and trusted structural engineer telling me a clear, and verifiable explanation of the cause(s) of the problem and a viable and affordable solution, 2) trusted and experienced tradespeople who would be implementing the solution (carpenter, mason, etc.) confirming with me that they could fix the issue (with 90% or higher confidence that the issue could be resolved within budget), and 3) confirmation from city inspectors that the issue (and an inability to fix the issue) would not result in condemnation/revocation of occupancy permits. ...and even then, I'd only proceed if I had the cash reserves to ride out a major series of unexpected problems (e.g.; time overruns, budget overruns, unexpected revocation of occupancy permits from the city, etc.) 

If the guest house was permitted , you shouldnt have to do anything . 

How difficult is it to just get the permit?

I am looking at 1.8 acre parcel where auto work and sales is permitted in the bylaw.

Is there a way to get a list of all permitted development projects ongoing in nyc?

Get permits if required.  

Also any cost that I may need to consider to pay upfront other than the land it self (i.e. survey, permits, etc)?