Hmm... I'm trying to do an upgrade to the most recent version of Wakaba, and I'm getting the same 500 errors: premature end of headers. Even when I do a fresh install and do the bare minimum configuration, nothin' but 500s all around.
http://www.pichan.org/newc/wakaba.pl

I don't see this line >>15 mentions in wakaba.pl... Did you put it there yourself? I haven't touched wakaba.pl (at least, where I'm trying a fresh install.)

WAHa, please, make this thing easier to install/upgrade already...