Updates:
August 27 (Saturday):
Engine rebuild complete. Brought the car home. Drove it on Sunday, clicking noise was there which we thought was related to AC.
August 29 (Monday):
Took it to the workshop, the mechanic disconnected the AC, started the car, the noise was still there. He said its not related to AC. He said the noise is comiing from the timimg chain. (during rebuild, we couldnt find the new timing chain assembly so we installed the used one)
Went again to the market and were able to find the new tensioner & the timing chain. We replaced it. The clicking noise went away. The engine sounded much better.
While driving the car back home, the engine light came on. Called the mechanic, he said to bring the car back in the morning
August 30 (Monday) Today:
Went to the workshop this morning. The scanner showed the following error codes:

The mechanic replaced the timing oil control valve. Again connected the scanner. All codes cleared.
Took the car for the test drive, after 45 minutes the check engine light again came back. Called the workshop, the mechanic said to remove the negative terminal of the battery, reconnect and start the car.
Drove the car for another hour, no check engine ight, the fuel average increased to 12.4 in the ciy with AC on. I never thought the mileage will improve this much. Engine sound is good. The drive is good.
The Total Cost
The cost shared previosuly was 129,300.
Today we returned the old parts and bought the new timing chain, tensioner and the Timing Oil Control Valve, the delta was 4,500
Total Engine Rebuild Cost so far: 133,800
Verdict
The verdict is still out, i will drive the car for few hours tomorrow to see if the engine light comes back.
The mechanic hasnt asked for his labor cost yet. He said to give him the money when i am fully satisfied with their work. The mechanic has been very cooperative. He dropped all his other work in the past 2 days to rectify the issues with my car.
In case the engine check light comes back again (I hope not), what would you all suggest?