I saw the game in question on TV and thought that it was handled properly albeit in a rather mucked up fashion.
Now as to whether or not it was handled correctly? I've no bloody idea. 
Personally, I would've reset the game clock to the time at which the last play ended, reset the play clock and started both with the RFP.
How do you know on the field what time was on the clock when the 1st down play ended? That's the problem. If it were later in a close game, the S checks everything all the time but even then with hurry up offenses, it's often impossible to get everything memorized and/or written down. Without that knowledge, you really can't go back to square one and start over.
TV shows the clock stopped at 8:42 for the 1st down. It obviously wasn't started on time because the offense is up over the ball and it hasn't started yet. As we know, in NCAA the R winds once the ball is spotted well before the offense, even this offense, is up over the ball. At this point we don't see the play clock on TV. Then on TV the game clock is finally started but is inexplicably stopped at 8:40 forcing the S to come in and discuss with the R resulting in the adjustment. So the game clock didn't start on time and when it started it was incorrectly stopped, two separate clock operator issues! Now where are you?
After the adjustment if the game clock is started on the ready, the offense could potentially use almost 60 seconds off the game clock without snapping the ball! The original 40 down to 5, then another 24. Not fair to the defense.
Then TV shows even after resetting the play clock to 25 and trying to get a play off, the play clock didn't start confusing the offense forcing another reset.
The games are hard enough without game and play clock goof ups and the fix it discussions, etc. will always look like a cluster.
