I’m not entirely sure what a chugging reaction is, but you mention that it is on overrun in lower gears which makes me suspect that a gear box mounting, engine mounting or engine stay has been incorrectly re-fitted or the rubber bush broken.
The effect will be most pronounced in low gears when the torque running through the transmission will be highest. When the clutch was changed they will have loosened or removed most of these items in order to get the gearbox off.