1. You have raised the said Black money through loan all in thousand or five hundred rupees notes.
2. Deposit the same with Bank disclosing that it has been taken on loan.
3. After that issue check to the builder for the said amount and he has to accept it since black money transaction will be stopped in India for good.
4. You can also pay exactly what has been mentioned in the agreement and if he refuses to register the sale deed after receiving the agreed amount, you can file a complaint case before the local District consumer dispute Redressal Forum alleging deficiency in service and unfair business practice praying for an order up on the builder to register the sale deed within next 15 days or pay a penalty of Rs.1 K per days delay with interest, damage and cost.
5. If you do not want to antagonise the builder, cancel the agreement and take back your entire amount paid to him.