I started to fall asleep reading that....
The motor will drop in using all your stock parts (tranny,axles,mounts,linkage,etc)..it's the same motor except 1.5ltr...
Switch the wiring harness from your old motor to the new one....and drop it in...
The ecu would have helped you when you do the auto to manual swap....it's the same as your except 5 speed....