OK, even though I elected to retire on August 25, I am still officially a member of TASO and my chapter, and my mind has not gone blank regarding football rules, yet. So, here I go.
There are few "absolutes" in NCAA football, but there are a handful. One of them is the game clock will start on the SNAP following any legal kick down. Period. Regardless of what else may have happened. End of story. 3-3-2-d-8
Another one is that the play clock will always be set to 25, and start on the referee's signal after a kick down (other than a free kick). (And, for those of you working UIL (Texas) football, even after a free kick down.) Period. Regardless of what else happened. End of story. 3-2-4-c-7 (For UIL, see Exception No. 33.)
No foul, no helmet off, no injury - nothing - will change that. Kick down = Play clock at 25 and on the ready, and game clock on the snap.
OK, the first scrimmage down following a free kick down, in pure NCAA football, will be 40, and start automatically when the ball becomes dead following the free kick down (if not governed by a penalty completion, a charged team time out, an offensive injury, or replay review).
Do some of the rules conflict? It may seem so, but the reality is that there is a hierarchy of those things that set the play clock, and a legal kick down is at the top of that hierarchy. "Why?" you ask? In NCAA football, what kind of teams are typically on the field for a kick down? Oh, yeah. Special teams. So, when the down is over, both teams, typically, will be sending in wholly different offensive and defensive units. The rules committee decided LONG AGO - well before the 40-second play clock - that this situation justified a stoppage of the game to allow both teams to make their changes, before the ball is declared ready for play. Since the game clock is not going to start until the snap, 40 seconds is foolish (at least it was until TV reared its ugly head and threatened to take their money elsewhere unless the NCAA cowed to their demands in search of the magic 3-hour window).
So, following a punt - even if Team A retains the ball - the play clock will be 25 and start on the R's signal, and the game clock will start on the snap. Every time. No exceptions.