One of the commands is the "Initialize All", which intends to be as
    close as possible to a hard reset on the all card. The PIC has full
    control over the several "peripherals", so I was thinking:

      Instead of jumping to the "Initialization" routine, why don't I just
    block the PIC, and let the WatchDog do the dirty work?

Does your initialization code actually do a hard reset of the devices?
We used to do something like this, and had an interesting set of problems
when the devices continued interrupting, and our system was in a piece of
code that no longer understood them (ie the "bootloader")  Some devices
rely on a HW reset signal to get reset, which may or may not happen when
you artifically generate a "system reset"...

BillW