there are much more plausible aircraft/missile conspiracy theories out there than TWA800.
A) an aircraft pressurized at 12000 feet is not the same as an aircraft pressurized at 35000 feet. One pops like a zit, the other doesn't.
B) if you're going to use a MANPAD on an airliner, you're going to want to fire from a position that gives you the best combination of security and a chance to hit. Why shoot at it at 12,000 feet when 6,000 feet gives you the same security and a better shot? Better still, why not shoot at planes when they're most vulnerable, right at takeoff and landing?
C) sorry, stingers are not designed to bring down airliners. That doesn't mean they won't, but they don't exactly have a charge big enough to tear the nost off a 747 at 12,000 feet.
D) long before they blamed the fuel tank on the mess, when they released the actions of the TWA 800 crew, they did mention switching over from the center fuel tank to the wing tanks. They also mentioned the temperature in those tanks. A heated fuel-air mixture doesn't need a stinger to set it off; a spark will do nicely.
E) Finally, why the "Accident" cover up? As our current administration has shown time and again, terrorism is a great excuse to squeeze the liberties out of the people. Why claim it wasn't a terrorist act when it was? To keep Americans from becoming fearful and agreeing to waive their rights?
F) If it was a US military accident, why wasn't it an Airbus like the last time? In any case, as long as the carrier is the same country as the military involved, you can still claim it was a terrorist act. That's what makes ustica a respectable conspiracy theory and TWA800 strictly amateur hour.