he said he would program the ECU for automatic??? The TCU gets bussed on the powertrain channel through the EIS - electronic ignition system - infact the EIS is the gate for all bus information throughout the car. Its pretty difficult to achieve a swap like this, mostly a car swap is a cheaper option.
Unless he has a whole car sitting which will be swapped into your car. Even the gauges are tied to the bus, vehicle mismatch creates problems.
Unless you have the factory linked stuff at this shop I dont see it happening reliably.
btw - the 6 spd manual is really nice to drive. The DM flywheel can be rebuilt - but not in Pakistan.