I've been thinking about his recently as I have ground the transmission several times while getting the hang of my new Corolla. I remember years ago when some mechanics took apart my rear differential and commented that there wasn'tt any "chipping." I've been imagining the gear teeth getting broken. So I'm glad to hear that I'm not destroying my manual transmission.
And kudos on teaching your son to drive a manual. I have my own ideas about cars and think they have become much too easy to drive, and much too easy to take for granted. The concentration required for learning a standard shift is intense, but as shifting becomes second nature, the habit of taking driving seriously remains, and the mind is drawn to different, less tactical and more strategic issues, like planning ahead, avoiding dangers, staying alive.
I've taught two kids to drive a stick and if I had one word of advice it would be not to comment on gear grinding -- they already feel terrible far out of proportion to any correction I can offer. It's easiest to find where the clutch engages while holding the car and then slowly going up a hill, letting it roll back under clutch control and easing it back up. I also learned they did better when I stopped talking and simulated dead air: what they will have beside them for most of their driving lives.
The intense pressure does create an opportunity to sear some simple messages into the highly receptive long-term memory (adrenaline does it). I said these just once or twice: "Maintain a space cushion, leave yourself an out, keep your eyes on the road but keep them moving, on the freeway look far ahead for dust or other barely perceptible signs of an accident, don't do anything but drive; don't eat, don't talk on the phone, just drive;, if you see a drunk, try to safely get past him rather than follow; bad driving can get you killed so keep learning."
It turned out that this was one chance to get these higher order messages across because a license requires only basic competence and then they calm down and head out alone (and like the rest of us, stop really listening once again). That's the scary time, and when you would give anything to have them back grinding the gears and listening to every word. It takes a year or so of worrying while they get seasoned at the wheel. I had one comfort: At least I told them all I knew about how to stay alive in a ca;, if they can get through this period, they should be pretty good drivers. They are and they can drive a stick like nobody's business.