Using NFHS rules:
4th and 17 and K's Punter gets roughed. Automatic first down for K. When does the clock start, on the snap or on the ready-for-play. Ref in game started it on ready-for-play. I'm unclear on this rule.

An NCAA answer is easy, on the snap.
For NFHS, rule 3-4-3-c says on the snap: "either team is awarded a new series following a legal kick".

Roughing the Punter
 

Mike,
The clock starts on the snap under both NCAA and NFHS football rules. Once the clock is stopped and the next play is not a free kick, it starts on the snap if an official's time-out is taken to award Team B a new series or to award either team a new series after a legal kick.