i think u shud ask sumbody who knows do it sir, did ur mechanic do any recalibration process when installing the throttle body tak?
for the second question, the flywheel cant be installed wrongly sir, screws in and dats about it. if u meant the clutch, den yes it can be out of alignment, but since there are so many things dat can cause vibration in the bay, one needs to experience it first hand before concluding anything sir