Hard to say on whether the transmission shop is off base because there are too many variables involved. It is somewhat true that people that have the PCS replaced may see it act up in the future. Worn out clutch pack is possible. The reason why the P1811 DTC sets is the PCM sees shift timing greater than .65 secs. When P1811 (max adapt, long shift) sets it commands maximum line pressure and disables shift adapts therefore you get the hard/harsh upshifts and possibly a whining sound. Checkout the thread below which may help out and possibly save you some money plus allow you to get some more mileage out of the autotransaxle. So far the fix has worked for many AF members.
Click here