I couldn't tell you what you were doing wrong, but you certainly exposed a problem during the process of rooting your phone with the current tools:
Rooting requires way too many independent moving parts. Ie, flashing recovery should also offer to root your phone if necessary. Obvious things like that are often non-obvious to the developers, as this is basically muscle memory to me at this point.
For what it's worth, the change I made to offer to root your phone will be going into the open source project, so it's not problematic with other users/phones in the future.
In any case, there is no manual, as I would hope that any software I write does not require one. If it does, it means I've failed :)