The vanilla kernel sources won't work, as they can't deal with Buffalo's ext3 byte swap. Use Sylver's SVN repository, or the "melfs" patch and genbako's kurobox patch; plus genbako's, Sylver's or my .config as the basis. Also make sure you have avr_evtd installed and configured. (You can find more information on all this in the forum and wiki.)
I would (shamelessly) recommend to install my kernel first (see http://hvkls.dyndns.org/downloads/docum ... aller.html
), not so much because it comes with over 900 modules to time and I could add yours if missing, but because this would also set up avr_evtd and modue-init-tools for you and adjust a few daemon settings. It would give you a working kernel 2.6 and a head-start for your own experiments.