The mod seems unable to operate correctly in server. In my server, the trip back from nether do not give player the Al Azif (the necronomicon). If I craft the book myself, when I open the book with right click, the HUD is empty. These will not occur in single player mode, so I guess if there are something wrong with the mod's performance in server.

That's weird, it never happened to me before. Is it the Overworld you're returning to? Are you using other mods?
In the meantime, you can use the command
/setplayerdata [USERNAME] add thebeginning
to get started with the research.
If you could send me the log file from the session in which this happened it could help, I'd be able to look for possible errors. If you don't have the means to do so then don't worry.