I diagnosed the issue to bad wiring as you know how desi electricians wire these engine. By the help of @Hassan1991, I got to know about ELS and I am 99% sure its not connected to ECU.
Even the electrician also removed the original AC amplifier (stolen) and connected AC switch directly to the ECU and also connected that switch to compressor (don't know exactly how, but it does cycle at low fan speed).
Today I also tried to get Fuel Pump relay connected the OEM way (previously it was hard wired to ignition with 2 3 joints and lower guage wires), FC - Fuel Pump Control should be through ECU, so I connected it. But the main power wire which goes to relay get power from EFI Main Relay but when I tried to trace wiring, I found out even the wire which should give ECU power when we turn on iginiton is also connected to ignition whereas It should be through EFI Main Relay and I didn't find any wire near ECU which shows continuity with EFI Main relay. So I connected fuel pump relay power wire to ignition wire because I was having no choice.
Similarly, the Altenator has a wire which is for ALT-S (sensing voltage) which goes through a 5A fuse located in the engine bay fuse box. It also doesn't show continuity.
So that's how the wiring has been messed up.
@Xulfiqar
AC Amplifier wiring cut:
Fuel Pump main power wire tapped:
MAIN Fuel pump wire naked:
Alternator Connector look how the wires are getting stripped:
