Noah, I feel your pain. The CODEX is back up at
www.first-codex.net, like Nate said.
I think the Master uP initialization routine is one of those things FIRST marks as "Don't touch! Don't move!", so I've never dabbled in that.
As for the SERIN/SEROUT stuff, I think there's already an article up on the CODEX dealing with everything you need to know about that (Maybe the IO shuffle? I'll check for sure later). It should help you out. If not, email me, and I'll post another article dealing with it.
The PBasic Field Manual has fallen by the wayside a bit, because I'm entirely too busy to write in it right now. It will be posted on the CODEX within the next month or two, hopefully, and I'll send you a copy via email if you wish.