Noises During Shifting problems of the 2011 Audi S4

My 2011 S4 started getting the "transmission malfunction continue driving" light at about 40,612 miles. At the same time my vehicle would jerk when stopping and acceleration. When shifting down the gears make a clunking noise specially from 3rd and 2nd gear. I was able to use my extended warranty that I bought because Audi didn't want to cover my vehicle. Audi service advisors recommend changing the mechatronic and circuit board but my warranty only authorized the circuit board. My vehicle still jerks when stopping as it downshifts and when I accelerate from a stop.