Considering the shifting problem, I'd suggest that you de-mod it because of the following TSB. No sense in having to argue about this if you don't have to. May not even be an issue, but why take the chance?
A/T - Shift/Driveability Concerns/SES Lamp ON
Bulletin No.: 04-07-30-013A
Date: January 25, 2005
Automatic Transmission Shift, Engine Driveability Concerns or Service Engine Soon (SES) Light On as a Result of the Use of an Excessively/Over-Oiled Aftermarket, Reusable Air Filter
2005 and Prior GM Cars and Light Duty Trucks
2005 and Prior Saturn Models
This bulletin is being revised to add additional model years and to clarify warranty coverage. Please discard Corporate Bulletin Number 04-07-30-013 (Section 07 - Transmission/Transaxle).
First, inspect the vehicle for a reusable after market excessively over-oiled air filter.
Don't Do This
DO NOT repair MAF sensors under warranty if concerns result from the use of an excessively over-oiled aftermarket, reusable filter.
The use of an excessively/over-oiled aftermarket, reusable air filter may result in:
^ Service Engine Soon (SES) Light On
^ Transmission shift concerns, slipping and damaged clutch(es) or band(*)
^ Engine driveability concerns, poor acceleration from a stop, limited engine RPM range
The oil that is used on these air filter elements may be transferred onto the Mass Air Flow (MAF) sensor causing contamination of the sensor. As a result, the Grams per Second (GPS) signal from the MAF may be low and any or all of the concerns listed above may occur.
When servicing a vehicle with any of these concerns, be sure to check for the presence of an aftermarket reusable, excessively/over-oiled air filter. The MAF, GPS reading should be compared to a like vehicle with an OEM air box and filter under the same driving conditions to verify the concern.
The use of an aftermarket reusable air filter DOES NOT void the vehicle'* warranty.
If an aftermarket reusable air filter is used, technicians should inspect the MAF sensor element and the air induction hose for contamination of oil prior to making warranty repairs.
Transmission or engine driveability concerns (related to the MAF sensor being contaminated with oil) that are the result of the use of an aftermarket reusable, excessively/over-oiled air filter are not considered to be warrantable repair items.
Black 2000 SSEi, Silverstar Headlights, Angel Eyes fogs, 3rd brake light overlay, hi-flo cat, drilled 180 degree thermostat, Intense FWI, PCM, shift kit, and 3.4 Pulley. Solid front mount.