I've never participated in the WCCC, but I guess the answers are the same as for most other computer chess tournaments.
bhlangonijr wrote: - The engine's programmer is permitted to operate the computer?
Yes.
- The computer operator must be affiliated to FIDE?
No.
- How is synchronized the chessboard clock with the engine "go" parameters?
Usually, the operator gives the engine slightly less time than on the board clock, in order to give himself some time to transfer the moves. For instance, if the time control is 30 minutes per game with 10 seconds increment per move made, I would set my program to a level of 25 minutes per game with 8 seconds increment.
In most tournaments, it is also possible to ask the arbiter for permission to adjust the program's clock during the game.
- Is it allowed to use xboard to serve as your GUI?
Yes, usually it is allowed to use any GUI you want, even if you didn't write it.
- if yes, is it allowed to enable xboard to play book moves instead of the engine?
I am not sure if xboard contains book code, but in principle you are right: It is allowed to use GUI book code, even if the GUI was written by somebody else. It is also allowed to use somebody else's endgame tablebase code, even inside the search. I find this extremely strange, but most people seem to like it this way.
Tord