You have not made a case. Everything you have said is not true.
Where does it say that the clock only stops when the whistle blows? It says "Upon a signal" which includes waving of the arms.The game clock operator shall stop the game clock (timeout) upon a signal by any official or upon the operator’s own positive
How long the entire play last is very important. There were 2:06 seconds on the clock, and you say the clock should have gone to 2:00, meaning all 6 seconds passed in full. You claim that the whistle blew 2-3 seconds after the clock had stopped. There are several problems with that. First, you have no clue when the clock actually stopped. (I do and will show you below) You can see it move to 2:01 and think that it stopped, but you have no clue how many tenths ran off before the clock was stopped. When the clock hits 2:01, all 10-tenths of that second have to pass before the clock moves to 2:00. We have 9-tenths of a second (nearly a full second) where we don't know when the clock actually stopped. It could have been stopped as soon as it hit 2:01, or maybe it didn't get stopped until it was about to change to 2:00 (5.9 seconds pass)
Here is how we can know. It can be proven when it was stopped by watching the next play. If it was stopped as soon as it his 2:01, then nearly a full second would have to go by on the next play before the clock changed to 2:00. If you watch the next play, the clock changes to 2:00 as soon as the ball is snapped to Tebow. This proves that the clock was stopped right before it was going to change to 2:00. (5.9 seconds)
You say that the whistle came 2-3 seconds after the clock stopped. That is impossible. I just proved that the clock was stopped after 5.9 seconds, and we know that we heard the whistle after 6.3 seconds. That is a difference of 4-tenths of a second, not 2 to 3 seconds.
We know that is not when he started since his hand is up in the air when we first see it in the video. He was out of the shot and is walking towards the players when we first see his hand in the air. He has to bring it up from his side to wave it in the air. It is very reasonable to assume that he started doing that at least 2-tenths of a second sooner then what we can see in the video. Remember, you agree that we can see him waving his arms at least 2-tenths of a second before we heard the whistle.
Just put all the evidence together.
#1. There was 2:06 on the clock, and from the time he enters the field of play to the time we hear the whistle blow is only 6.3 seconds.
#2. We know the official was waving his arms before we heard the whistle blow.
#3. We know 5.9 seconds ran off the clock since the clock immediately changed to 2:00 (as soon as the ball was snapped) on the next play.
#4. The pictures show the Jets having possession and being touched down before the official is seen waving his arms.
There is no evidence to prove that the clock should have gone to 2:00. There is plenty of evidence to prove why it should have stopped at 2:01.