Mike,
I can't really help except to say I got my custom board made following the instructions so it can work.
Seems like I looked at the provided examples.
I don't know for sure but I think its a minimal config thats used just during the early bootstage? At least I hope you don't have to go to all that trouble just to (pre)specify the sysclk
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/smile.gif
I'd like to get an explanation from Altera, because I don't see any big purpose. It uses the EPCS so the pins and all the workings are not negotiable.
Ken