Well, I am starting to port the code over to the chipkit Uno32. First I had to port the library back to Arduino 0023, since that is what the chipkit software--MPIDE--is based on. This was mostly just changing
#if ARDUINO < 100
as well as converting the examples from .ino back to .pde files. After this massaging, I got it to compile in 0023.
The code is not pretty at the moment since I am using a lot of "#if defined (__PIC32MX__)" to switch between AVR and PIC specific code. I have the SD card library working on the Uno32, so now I need to port over the PWM.
I am running the SD card at 400kHz during initialization and then at 20MHz for everything after that. It is looking like the PWM will be sampled at 78125Hz for full rate and 39062.5Hz for half rate. These values were chosen to give perfect 8bit resolution on the PWM and still be close to the original 62500 and 31250Hz values.