My son just bought a 2005 G35 coupe 6MT and I drove it from the seller's house 4 hours back to my house with no problems whatsoever. Shortly after, I took my son out to learn how to drive stick in an empty parking lot. We practiced on a hill and spent about a half hour working the clutch pretty good. He hardly made any mistakes.

I drove the car back to my home and on the way back we experienced a startling jolting noise/feel when in second gear. It felt like someone was popping the clutch in and out but the engine was in 2nd gear and I was not touching the clutch at all.

I am thinking that the clutch and plates were just over heating from a combination of the long drive and teaching manual to my son. I know the car has zero problems because I have known the seller for a long time.

Any input guys?

I was going to say let it cool down over night and drive it the next day.

took it out earlier...just fine

Good. You just worked it to hard

Yeah they tend to get hot after prolonged use or running the car hard such as burning tires and what not really gets that clutch baked!