is the car automatic or manual - manual with the new clutch I presume

Is this at a dealer?

did he ask you to bring the car back in?

did he say he wanted to test drive the car?

think about this, transmission get removed from car: drive-shaft gets shifted back or removed, flex disc gets disturbed, transmission mount gets removed, connection between engine and transmission gets disturbed, input shaft to torque converter ( clutch ) gets disconnected, vacuum lines get removed, linkage gets disconnected, with a flush crude can get dislodged.

everything get reassembled, alignment of all rotating masses is important.

I would think the car gets put back on the lift and while up there the minimum thing to do is get the car running, check for vibration. Then you'd do a second trans flush to see if things clear out.

manual are robust so I would think about clutch alignment, driveshaft alignment also on a car with this mileage it ignition wires/accessories are old and get disturbed could be a culprit.