vice-setup won't run with the server.conf.ex file in the /etc/ directory. /etc/cipe needs to be created and the file placed in that directory for cipe-server to be setup sucessfully.
woops. /etc/coda needs to be created, not /etc/cipe - my bad. ;)
This is really a bug in the coda Makefiles (specifically, in the file configs/Makerules, lines 157-164 in version 6.0.3). I am not proficient enough with GNU make to really understand what is going on; perhaps someone can look at it? It appears to do some kind of test, then places the config file in the wrong place. I'm (finally) finishing an ebuild for 6.0.3; I'll make sure it gets put in the right place in that version...
Hopefully fixed in the 6.0.3 version committed. Any problems add to bug http://bugs.gentoo.org/show_bug.cgi?id=26132