You will need to replace the starter motor, because of it being mounted behind the engine on automatic models, instead of over the manual gearbox. It will obviously also rotate in the opposite direction.
The bolts fastening the "flex plate" onto the crankshaft are shorter than those fastening a flywheel on manual gearbox models.
I own a Daihatsu MOVE of which is an automatic, after having previously owned one with the 5-speed manual gearbox. For urban driving, I much prefer the automatic over the long-legged 5-speed, since our speed limits here are incremented to mostly 30, 50 and 70 kilometers per hour of which the gear ratios designed into the 5-speed boxes do not coordinate well with these speed limits, resulting in requiring use of lower gears of which increase fuel consumption and engine wear.
If it were a question of Daihatsu and their in Pakistan under license built models instead producing these vehicles with 6-speed gearboxes, using the automatic gearboxes would have been rather obsolete.
In any event, I don't understand why the thread author wishes to retain the manual gearbox. If properly maintained and driven, the automatic boxes are virtually indestructable and trouble free. Clutch assembly replacement would be non-existent. If I were the author, I would either obtain all necessary bits for a swap from a breaker yard or organize a swap with a vehicle owner who has an automatic and wishes to instead drive his vehicle manually-shifted.
A PDF manual for the fuel-injected version of this vehicle is available as a ZIP download, upon request. Therein, detailed information required for a swap is to be found