"Poopping" the clutch to stop the engine could definitely damage an older flex disk. That's a lot of mass and inertia to sudenly bring to a halt. They could have easily done it by simply blocking the air intake. Would've taken a few seconds longer, but wouldn't damage anything. I think they might owe you a freebie repair. As to the linkage, when mine went out it did affect the shift linkage, as I recall. I believe it bent something in the linkage so that the shift lever didn't sit properly in the detent in the shift gate when in the appropriate gear. It would make sense that if the flex disk/driveshaft assembly was wonky and spinning out of round, both the driveshaft and trans tailpiece would be trying to rotate counter to each other (Newton's Third Law). That would certainly account for the banging noise and the scraping. There isn't much clearance on the sides or above the trans as I recall and perhaps something got moved or bent out of place.

Gary