Hello Chris,
The FlexTimer is built upon a simple timer, the HCS08 Timer PWM Module – TPM, used for many years on Freescale's 8-bit microcontrollers.
Unfortunately there is no a document that shows the mapping of the old PWM registers to the newer FTM registers, but I recommend the “Migration Guide from S08 to Kinetis E Family” document, specially Chapter 13.
This application note outlines the key differences between S08 (specifically S08P) and KE product families, and provides code conversion recommendations to help shorten the learn curve.
Please find the document mentioned above in the following link:
http://www.freescale.com/files/32bit/doc/app_note/AN4757.pdf
Hope this information will be useful for you.
Have a great day.
Best Regards,
David Diaz.
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