1)your father can issue legal notice to builder to execute registered sale deed for 2 flats and 2 shops
2) if builder fails to do so your father can file suit for specific performance .to direct builder to execute registered sale deed in his favour
3) suit for specific performance has to be filed within period of 3 years
4)on your father demise you can make application to court to be added as party to suit along with other legal heirs
5)if copy of draft deed has been forwarded to builder it would be proof that there is no delay in your part
6) for registration of document both parties have to attend court and submit document for registration