First big thanks to FFG for getting these answers out, and to Adam should you go home it's like 10pm in your timezone, but thanks again.
1) "Can a Bonus Token replace a Special Object?"
Yes, there is nothing in the rules preventing this.
2) "Does the Trench Gun only do damage if you cannot move the target equal to the amount uncanceled successes, or does it do damage as on page 22 like a normal weapon?"
The trench gun does damage just like a normal weapon. The movement penalty produces additional automatic wounds that are added to any damage dealt as normal.
3) "Can Hoax be targeted by weapons, etc, that do not require Line of Sight, such as Doom, Patmos Amulet, Atheon, Sha-Na-Ra?"
While invisible, Hoax cannot be targeted by enemy characters. This includes abilities that can target characters out-of-path, such as Doom, Patmos Amulet, Atheon, and Sha-Na-Ra.
Well there you go I hope others are getting answers soon, and I hope this points to an updated FAQ soon.
Thanks again to Adam from FFG.