Where are the rules for the Assassin located?
Rules for the Assassin are not consolidated in one place - instead they are spread out throughout the rule sheet in little green boxes, with the special rule described at the point where it comes into play. Each of these little boxes starts with "Assassin" so you know that it only relates to the expansion.
My suggestion is to play without using the Assassin card initially, and to learn the game that way. After you are familiar with the game, then you can add the extra card to the deck and go over the small rule changes before starting so that players will have something else to think about.
What's up with the bonus points for not being discovered?
The player who is dealt (or who later draws) the Assassin card has slightly different rules for dealing with clues and end of game scoring.
The Assassin player isn't required to play a clue from his hand if he has a set, allowing him to withhold information from the table and have a better chance of guessing the three removed cards. However, he may want to play clues because every clue played by him is worth a full point. To make playing clues more tempting, the Assassin card itself can always be used as a wild to create one extra clue.
End of game scoring is slightly different, because there is also a bonus given for guessing the Assassin player or for the Assassin staying hidden all game.
I posted some other thoughts about the Assassin role here, but haven't heard much response:
My guess is that most people are either playing with smaller groups or just haven't started using the mini-expansion.
For what it's worth: For people who didn't get the ? Suspect card for KickStarting the game, the Assassin card does work nicely as a stand-in for that card (as you suggested in the initial post). In this case, just treat the Assassin card as a wild card that matches any number and ignore all special Assassin rules. You don't need 5/6 players to use the card in this way, and it will make playing clues easier but tracking information more difficult.