That's rough Sherpa. I'm guessing that you're gonna need to cut a hole in your roof for the vent hood, and obviously tap into the plumbing for the mop sink. I'm sure local regs vary but the Certificate of Occupancy is probably required as a way of completeing you building permit. We were a new construction, but it seems like we had to get everyone from the fire marshall all the way down to the dog catcher to sign off before we could get our C.O.
You may already be trying this, but I do have a couple of things that MIGHT help. You may be able to negotiate with the architect. We didn't shop around, but we felt that the architect's original bid seem WAY high. With a friendly but firm phone call, we were able to knock off about 30% of the fees.
Another thing to think about... I you use an architect and a contractor that have previous experience with this type of job around your municipality, they might be able to streamline the process. Might not save you money on the front end, but if you have a projected opening date, and that date needs to be delayed due to failed inspections, it will cost you revenue dollars.
I hope it all goes well for you, I know it's no fun dealing with bureaucracies.