I have one question:
What are the differences between NCAA and NFL on the last two minutes?
When will the clock run or stop?
Special:
QB Sack in NFL?

I can't speak about NFL rules though I know that there are a number of differences for timing rules near the end of the half/game. <b><i> MJT...maybe you could help here since you use NFL rules in your semi-pro games.</i></b> However, NCAA has no special timing rules near the end of the half/game. The clock continues to operate as it does in the middle of the game.

NFL timing rules are very different than NCAA or NF. Here you go.
They use a 40 and 25 second clock depending on what happens during and after the play.
40 second clock is used after a normal play, whether it is a run (in or OOB’s) or a pass (incomplete or complete). At the end of the play, when the ball becomes dead, the covering official will raise his hand, signaling the DB spot, also indicating that the 40 second clock starts. If at a game, you will see this clock start at that time and count down from 40. I love it, as the R, cuz I do not blow a RFP on normal plays such as these.
25 second clock is used after a penalty, TO, COP, injury, play review, or any other long stoppage. This is like a normal NF, or NCAA RFP.
Timing is also very different in other situations. On a run OOB’s the clock starts after the ball is spotted. The clock does not stop on 1st downs. The clock will be wound after ALL penalties after blowing the RFP. The clock stops after a QB sack until ball is spotted, and then it is started again.
The timing stays this way until the last 2 minutes of the 1st half, and last 5 minutes of the game. The NFL wants the game to go as quickly as possible until these 2 times, then slow it down dramatically for the “important” part of the game. Then some of the timing rules change to slow it down. Clock starts on the snap now for; run OOB’s, after a penalty, forward fumble OOB’s, and the clock does not stop now for a QB sack. So the last 2 minutes of the 1st half, and last 5 of the game take quite a bit longer.
Also in the last 2 minutes, all TO’s are 30 seconds. In the last minute, a foul by the offense which stops a running clock is a 10 second run off – but if the offense has a TO, they can take it and not have the runoff.

Hope that answers some of your questions.