I have decided to go for swap after checking part prices needing for rebuild. I have swapped the engine with L15A2 (i.e., iDSI) that has probably come from a Honda City or Fit Aria of Malaysian origin. Got it for Rs.26K from Mitho Khan ahata in Saddar Rawalpindi with swap of old engine. Got it complete with wiring but without gear.
With prices this cheap, I believe it is waste of time to worry/money for rebuild of iDSI engines, and even then there is no guarantee that crank noise etc will go away.
We fitted it at home and Alhamdulillah started with first self this very evening.
I think I will post a separate thread for the topic for others to take help.