Clutch pedal stop adjustment

2D, single disk, Honda 3.5 . I think I wore out my previous clutch by not having the slave cylinder set nuts adusted correctly ( to tight , throw out bearing riding on the clutch fingers ) and over extending the slave cylinder/throw out bearing (no pedal stop on previous pedals). New throw out bearing, new clutch, and new pedal assembly with a set screw pedal stop for the clutch pedal. I read about the 1/4" to 3/8" free play for the slave cylinder. How do you set the pedal stop so you have enough slave cylinder throw to engage the clutch but not too much to over extend the throw out bearing?

Push it in with the engine running, slowly let the clutch out until it engages and have a helper mark it?

I've never had an issue with it over extending when adjusted to the correct freeplay. That slave cylinder doesn't have a huge amount of travel.