Agreed. I spent way too much time reading old mailing lists and server and client specific docs when trying to understand the protocol (not any specific software that used it) while writing nodebot (http://github.com/thwarted/nodebot). RFC1459 is seriously lacking in real-world use, explanation of terms, and general robustness, despite that it was written to document a defacto protocol.
On the other hand, you do see a lot of the organic evolution of a protocol in what is IRC, which is valuable from both an historical and educational perspective.
I agree about the problems with the specs. For the most part, the best way to find out how a lot of the stuff worked was just to telnet a few IRC servers. For example, the thing about some servers needing a ping after user? Not mentioned in any spec, discovered while using a specific IRC network via telnet.
On the other hand, you do see a lot of the organic evolution of a protocol in what is IRC, which is valuable from both an historical and educational perspective.