Are you sure the contractor you hired is even a licensed contractor? If he is then great, you can give his name and license number to the inspector and he can do whatever is necessary to get the work cleared up and permitted. If not then this is going to be a big headache on you.
This is also a lesson for you, you need to learn to stay on top of things. As an investor you need to verify that what is being done is what you paid for. If the buyer can look up the permits then why didn't you? Here I can see everything online, permits, inspection times, inspector's comments, etc. I don't issue final payments until I verify that the permits have been closed. I also verify that the contractors have pulled the permits when they are starting the work because as the owner I am going to be the one with the issue if the property gets nailed for work without a permit.
At this point you're going to have to pull after the fact permits. I don't know about your city but those are generally far more expensive and if some of the work needed to be inspected before being closed up then it will have to be opened back up if the inspector needs it opened (things plumbing or electrical). HVAC is easy enough to inspect after the fact. Electrical it depends on what work you did. If it's just a service upgrade or panel changeout that's easy but if you rewired the entire house you could be in for a big headache.