Amnesty scheme

In Amnesty Scheme in Maharashtra, stamp duty and penalty has been paid on agreement to purchase in 1996 and JDR has issued certificate to the effect. However the document has not been registered uptil now. Agreement is in between Developer and Purchaser. Co.op. Housing Society has been formed and developer has expired thereafter. Now purchaser wants to register the agreement by paying latest stamp duty as per market value. Which document he should prepare for registration of the above agreement? Declaration, Confirmation, Sale Deed or any other document? Experts are requested to kindly advise. Thanks.