Problem solved,

I found that I could enter 125000 Hz in the HPWM command if I set the compiler to long words. When the 125kHz gets multiplied by 16 due to the 64 MHz PLL clock I get 2 Mhz output on pin 13, just what I needed!

Not sure why the register setup method does not work, but I am moving on for now.

Regards,

-Tim