Following clauses should be made in clear terms.
Time completion period with stage wise completion.
Progressive payment clauses.
Time is the essence of the contract must be written.
Clear terms of compensation for any delay in completion.
Clear term under what circumstances contract can be rescinded.
Arbitration clause if you want to avoid litigation.
Advance payment and security clauses.
Quality of work as per standard specification. Can here refer CPWD specification.
A joint measurement clause.
Clearly define force majuere condition.
Clearly mention the defect liability period.
For proper safety bank guarantee can be taken for any advance payment and for security deposit.
Retention money clauses to release retention amount after successful completion of defect liability period.
It better to draft the agreement by any lawyer.
Other general point.
Agreement need not be registered. Make it on stamp paper. May be get it notarized. Witness by one or two is good.
Payment can be made to any one. Clear authorisation to this effect shall be made in agreement.
Further now after RERA, you can adopt necessary format of RERA agreement suitability.