The Pinion Factor is the thing that needs to be programmed on the 5-speed.
1. Turn the ignition on with the transmission in neutral.
2. Use the DRBIII and select THEFT ALARM, SKIM then MISCELLANEOUS.
3. Select PCM REPLACED.
4. Enter secured access mode by entering the vehicle 4-digit PIN.
5. Press ENTER to transfer the secret key (the SKIM will send the secret key to the PCM).
This is from the 2003 Powertrain Diagnostic Procedures for the PT Cruiser, Section 3.2.9, pages 11 and 12.
Under the same section:
"The SKIS Secret Key is an I.D. code that is unique to each SKIS. This code is programmed and stored in the SKIM, engine controler and transponder-chip (ignition key). When replacing the PCM it is necessary to program the secret key into the PCM."
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The PIN should be on the label of a plastic bag that is with your owner's manual packet. It is the bag that the spare ignition key came in.
This procedure may have been updated, but this is how it is presented in the Diag manual. I believe, that if only the PCM is changed, the SKIM will verify it to be legit by comparing the VIN in the PCM to the VIN it has stored, and not require the step of having to enter a PIN. I think that is only necessary when the PCM and SKIM are changed at the same time.
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