Hi Todd,
It is not as difficult as you imagine to make a target board. Just follow the instructions of mk_target_board command till you get the SOPC builder system which is automaticlly generated.
Do not add or remove any component from the SOPC Builder system. You will see the ASMI component, let it be. EPCS controller=ASMI+bootloader, but here you need not EPCS controller. mk_target_board is only needed when using flash programmer under Nios II IDE. It is used to burn your hardware and/or software image to FLASH, and has nothing to do with your "real" application.
If you do want to modify the SOPC Builder system, you can reduce the buffer size because there is maybe an error on the document.
Cheers,