Hello Brian,
Indeed, using the default jumper settings from the document mentioned above, the bootloader runs on the MCF51JM128 daughter board.
Please try creating a new CodeWarrior project, using the documentation from the AN3748:
http://cache.freescale.com/files/microcontrollers/doc/app_note/AN3748.pdf
Chapter 3 explains how to create a new MCF51JM128 project which supports the USB bootloader.
Please note that you need to download project JM128_BootLoader_Framework instead JM128_Boot_Lib in order to add the source files.
Hope this information will be useful for you.
David :smileyhappy: