You have to pay fresh stamp duty and registration charges 

Since the validity of Rent Agreement is still subsisting for another 2 years, there will be no need to pay fresh stamp duty and Registration fee for the MOU. Only if there's change in the Lessor and/or Lessee, you need to pay fresh stamp duty and registration charges.

Yes you need to pay for the amended or supplementary agreement but it will be negligible amount

Dear Sir/Madam,

It is suggested that you can do the said amendments on the stamp paper of Rs. 200/- only. 

You can execute a rectification rental agreement, however whether it will be effective after three years of original deed's execution is to be enquired from the registrar's office.

Alternately you can execute a supplementary rental agreement by an unregistered deed incorporating the changes you desire to have it now.

Or you can mutually cancel the original rental agreement and enter into a fresh rental agreement but you may have to pay the stamp duty afresh accordingly.

- Since, the current agreement was signed for 5 years , then you cannot registered or rectified the same agreement on the condition of rectifying the same. 

- However, you can execute Supplementary rent agreement after mentioning the details as you mentioned above. 

- Otherwise , you can cancel the current rent agreement mutually , and registered a fresh one. 

Execute fresh agreement and pay stamp duty and registration charges.