if the documentation is in order, then go to the nearest police station and lodge a cheating case against the dealer immediately. Once this is done, intimate the RTO the entire story that you under went, tell them you are willing to co-operate in the case to the fullest.
Handover the car to the police station and collect a receipt for the same.Future complaints against the car will be avoided and for the past complaints pending on the car you will not be penalized. Produce the receipt as on the date when the car was picked up by you from the car dealer.
If you have to recover all the amounts from the fraudulent car dealer then you may have to file a consumer complaint against his agency in order to recover this amounts with interest and compensation as well.