Hi Guys,
After some searching I found a way to shut down a lot of the noise generated by the MCF52259!
Shut down the PST[3:0] pins, i set them to outputs and set them low
PDDPAR &= (~0b00001111);
DDRDD |= 0b00001111;
PORTDD &= (~0b00001111);
turn off the PSTCLK pin so it does nothing
SYNCR |= 0x0040;
There is a newer version of the MCF52259 reference manual, I was using V1 which is missing some information, V4 has more information.