Here is a copy of a Saturn TSB regarding harsh shifting:
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BULLETIN NO.: 01-T-09
SUBJECT:
Harsh Shifts No Shifts, and/or No TCC Operation with Transaxle Related DTCs Set (Replace Transaxle Connector and Harness
MODELS AFFECTED:
1994 - 2001 Saturn S-Series vehicles with automatic transaxles (RPO MP6 or MP7
CONDITION:
Some customers may comment about harsh transaxle shifting and/or erratic transaxle shifting. One or more transaxle-related diagnostic trouble codes (DTCs) may have set. The Malfunction Indicator Lamp (MIL) may or may not be illuminated depending on what DTC is set.
Images available only to Customers.
One or more of the DTCs shown may be set and indicate what circuits are affected
CAUSE:
Due to normal powertrain vibration, the transaxle wiring may flex and cause a circuit to open inside wire insulation near transaxle connector. In some cases, insulation will look distorted at point of open circuit
CORRECTION:
Perform procedure in this bulletin to replace transaxle connector (P/N 21024415).
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As noted in the TSB above, Saturn has had some problems with the electrical harness inside the transmission causing harsh shifting such as you describe.
The other likely cause is still a valve body problem; I would return the vehicle to the shop that performed the valve body replacement and let them continue diagnosis of the problem. if they are stumped, the Saturn dealer service department would be the next place to go; they likely see this problem often and also have factory technical assistance available for tough diagnostic problems.
I hope this is helpful to you!