I do not know if that aircraft was specifically targeted or if it was just a target of opportunity. If that aircraft was the specific target, an hour's wait is nothing.
2. From what I've read, Flight 800 was actually flying lower than usual that night through the area, having maintained a lower altitude to make way for a northbound aircraft flying into Providence, Rhode Island. Nobody would have been able to predict that.
I wouldn't presume to know the missile's upper threshold of reach. It may have been good up to 40,000 feet for all we know. Jack Cashill has done some investigation as to the type of missile he believes is involved. I will have to suggest you look up his research on the subject.
3. Shooting a missile at an aircraft flying 15,000 feet overhead from a point that far east makes no sense if you're doing it from there to avoid getting caught. At that altitude there's a serious risk that the missile won't hit its target -- which means you're running the risk of getting caught without any certainty that your plan will even work.
The transponder was pinging from the aircraft. I don't think tracking it was that difficult of a problem.
The last recorded radar transponder return from the airplane was recorded by the Federal Aviation Administration (FAA) radar site at Trevose, Pennsylvania at 8:31:12pm
The transponder only pings when it is queried by a proper signal from the active radar on the proper signal. That signal swept the plane about every 4.64 seconds. The missile, if there was one, was traveling at Mach 2 or greater. At that speed, the missile would travel almost a mile in the 4.64 seconds and there would only be time for any such missile to get just two transponder returns during the flight, not enough to use for any lock on the plane for guidance. Most of these MANPAD missiles are heat seekers and would then average the center of the heat sources when they get close enough.
Flight TWA-800 at 13,800 feet was visible by the naked eye at 8:31 PM on that July evening from the range this theoretical missile could be fired. It was at the extreme altitude range that could be reached by some tripod launched missiles, but not by any shoulder launched missiles.
TWA-800 was also being tracked by two passive radar stations, but the records of those radar stations were taken to the White House the next day and have never been seen since. One of them was a much more rapid sweep. Those records could have told us a lot of the missing distance data and possibly some altitude data and certainly would have shown data on any bogeys that might have been in the area. The Active Radar return pings do not record any data not related to transponders, unfortunately. The air traffic controllers do not need to have their screens cluttered up with data they are not concerned about so their systems are designed to exclude everything except air traffic data.