Hi Kevin
Choose a low frequency clock for the FlexTimer if possible and use maximum pre-scaler too; this will give you longer periods for the PWM period.
You can also use an external clock which allow even slower clocks.
It is also possible to use two FlexTimers (cascaded) - the first generating a slow clock for the second (this can also be cascaded via the FlexTimer clock input).
Regards
Mark
uTasker developer and supporter (+5'000 hours experience on +60 Kinetis derivatives in +80 product developments)
Kinetis: http://www.utasker.com/kinetis.html