Owner name changed legally between agreement to sell & sale deed

On the basis of the documentary evidences your change of name has been established , hence there is no infirmity in proceeding with the payment of the stamp duty on the new name. 

You have stated to have paid Rs. 1.53 lakh for stamp duty from your wife's account, there no issue / ambiguity / problem. 

Subsequently remaining stamp duty of Rs. 3.72 lakh is being paid from your new name. 

Can stamp duty be accepted in parts ?

Facts posted are vague and confusing.

Yes stamp duty is getting paid in two parts one part was laid when i booked the home and ATS was executed in 2019 and mow last week i paid balance 3.72 for getting registration which will be done this week. Only concern is that builder also doesn't have full confidence will the last part paid in old name will be considered by the registrar. Some people are saying will be considered bas person is same and home is same so should not be issue but I was getting some doubts. Thus wanted some expert opinion.

As it is there are two persons involved in this purchase of property.

You are creating unnecessary problems for yourself without understanding the facts 

The name change evidence is already there with you, hence there is nothing that is concerned about it in this connection.

You can proceed with the proposed balance of stamp duty payment in the new name itself.