Hi
I'm in the same situation as you but a bit further working on usb now
I've Got UART I2C working fine as well as PIT and DMA timers.
To initialise your board you've got to
init all what you need using functions from mcf5222x_sysinit.c or writing your own.
Make sure all your support Files (Support files folder in project) are targeted .
Make sure you're GPIO registers are set to use Switches (switches are set to GPIO inputs by default so it should be ok if you haven't modify it) .
Do you reach the interrupt handler if you set a breakpoint in it?
Do you see if your Pending register from the interrupt controller acknowledges Interrupts?
if Yes does your Mask register mask the interrupt ?
Let us know
Olivier
PS: HID usb example is a good source od information.