Hi there MiB and welcome to the game!
Unfortunately yes, when Call of Cthulhu was re-released in the current Living Card Game (LCG) format, Steve Clarney was misprinted as an Agency character. (Originally, in the CCG days, he was a Miskatonic University character
Fantasy Flight Games have chosen not to correct this, so Steve has defected and is now affiliated with The Agency. This means that Miskatonic University is one card short and The Agency has one extra in the Core set, but that doesn't significantly affect the game play (as you'll find you're playing with decks that are a few cards short of the tournament-required '50-card deck minimum' anyway).
You're also right that, when setting up, the rulebook says to choose two factions and then add six neutral cards each: F141-147 for one player and F148-154 for the other, which excludes The Bootleg Whiskey Cover-Up (F155). I'm not sure if this was intentional, for people to play their initial games without any Conspiracy cards to reduce a bit of complexity, or if it was an oversight... but feel free to add it in too if you want to try it out - perhaps flip a coin to see who gets to include it in their deck, or you could always draft the neutral cards individually (instead of choosing between the two half-sets).
Instructions on how to use Conspiracy cards are detailed on Page 11 of the rulebook.
Edited by jasonconlon, 14 July 2014 - 08:07 PM.