Late property registration process

My father bought 1000 Sq yard agricultural land in Haryana in year 2000 and got land registered. In 2005 my father bought adjoining 150 Sq yard land from same person but didn't get the paper work or property registered In his name and now in 2016 we want to get the property registered with seller being good is agreeing to help in registration process. I've following questions 1. In 2005 , we paid 3 lack in cash to purchase 150 Sq yard but now the collector rate for same is 10000/Sq yd. Do we have to show a sale of 15 lacs to seller by paying him check in order to pay stamp duty of say 6% which will be approx 90000(15 lacs*6%) or should we just pay stamp duty without any supporting financial transaction of 15 lack. 2. If point 1 doesn't work then is there any way to pay penalty for delayed registration of property. If so then what's the approx penalty charges.