Faking evidence is quite another, and you have to remember the few at the top that know about the whole thing aren't the kind of people that can sneak in to Boeing and knock out some time-change parts.
Balls.
If it was a cruise missile (one suggestion) or a drone plane then you'd have to keep quiet:
1) The crew of the launcher that fired off the missile
2) The stores department that accounts for the missile
3) The team that collected parts and investigated the crash
4) All arms of the investigative machine that collected data.
5) Anyone who saw the orriginal plane being shot down (the alternative explanation)
6) Anyone who (re)armed the plane that shot the orriginal plane down
7) The pilots of the planes that shot the orriginal plane down.
8) (If not a cruise missile but a drone plane) The team involved in flying it, refitting it, launching and test flying it etc.
You can't say that only a few people would be in on it, cruise missiles aren't one man portable toys that the military use all the time, nor are FAA investigations one man efforts, surely one of them would have said that the plane was a fake?
As you'd have to have members of the accident investigation crew in on it they'd be able to sign out a few old bits of 757 parts and singe them, no additional people needed. It would also have prevented this line of enquiry too.