I think the frames work well. If (hopefully) this place gets mad popular like 2ch, a ton of boards will be needed, so a list along the side is the best way to go. A toolbar would be cool too, but I think right now an FAQ is needed most so new users will understand the details of posting.

Even adding a link directly to http://wakaba.c3.cx/docs/docs.html#UsersGuide would help, I think.

I think the ID system needs to be explained a little though, and maybe the policy of logging IP addresses as well.