Hi John,
I have delved into this and it seems this application note has not been migrated to the newer silicon revision.
My humble suggestion is the next:
As you can notice, the application note uses the USB stack. Then I would migrate first an example of the USB stack for this TWR system.
And then use the application files like the Loader.c and main.c.
Of course this is not an easy task because there has been changes between silicon revision of the TWR-K60N512 and TWR-K60D100M.
I am going to try to get an example of the USB stack for new silicon rev.
Regards,
Alejandro