I got my EGR pipe changed a few days ago and my Boot for the rack and pinion.. ALso got my motor mounts and tranny mounts retightened along with resealing of my oil pan.. after 480 buck parts and labor

my engine shakes really bad in D @ stop.. and shakes up to 50mph. Also there's a "kick" when shifting from 2 - 3 and 3-4... as if there is too much throttle or sometin..
my mechanic told me the 3 sensors, TPS, idle and another have to be recalibrated because the previous mechanic adjusted those sensors in order to compensate for the leak in my EGR pipe..

does any of this make sense? I called lexus and they told me its my tranny and engine mounts but those were solid on my car..

Any ideas on what I should do and the costs? any help would be nice.. by the way.. EGR replacement really makes the engine quite down