@star2
Well..... after fixing fan's grounding and using the multimeter on some ECU wires, the fear that I'll either melt the ECU or myself is gone, Alhamdulillah 
So with one of my biggest wishlist of running the fan on auto through ECU, I decided to give it a try today.
First thing I wanted to make sure was the proper working of temp sensor. So studied the manual, disconnected the fan, connected the multimeter to pin 54 and was happy to see the reading starting from 2.7 and go down to 1.7 in small steps of around 0.05V. So concluded that temp sensor is working fine...
Now i expected 12V on pin 14 when the engine is cold. To my disappointment, it was unstable between 0~250 mV.
So got back to manual to find out that Refrigerant pressure sensor also has a role to play. With AC OFF, it was supposed to give 12V, and with AC ON, 0V.
But it's giving 5V :S. What could be the reason for this 5V?
Now I've put it to tomorrow to check the location of the sensor. If it exists in the first place, then fine. Else, I'm planning to give 12V direct from battery to pin 109, so that AC input is bypassed.
What do you suggest???