[Motofool]

Great advice, @choneofakind !!!
Manual transmission cager + pedaling bicyclist = awesome motorcycle rider

Originally Posted by Flawed

.......However is there a down side to using the clutch to stop the bike?
Nope. Remember that I told you that your left hand is your friend and whenever in doubt, just clutch-in?

Does it wear down badly on the bike somehow?
Nope. There is a bearing in a bath of oil preventing that from happening. Your left hand may get tired after a while of pressing that lever against the force of the clutch's springs.

The proper way to stop a red light would then be...

1.) Slow down. Closing throttle and gently applying rear brake (only rear brake for now and always if turning).
2.) Pull clutch in.
3.) Let the throttle off completely. Done in 1) above in order to use some engine braking effect.
4.) Switch to neutral (not sure if step 5 should go before step 4? I guess it could be done both ways but one is more proper?) Come to a complete stop, put one foot down, keep clutch in, shift into neutral if you will, clutch-out.
5.) Ease into the breaks until stopped. See 4) above.

This way when I let go of the clutch the bike wont go anywhere and the engine will still be running... solving my stalling problem.
If you are on a hill, you will need to keep braking until you take-off again.

Would you use just the clutch at something like a stop sign for a quick stop? Or is that not good, a bad habit to get into? Or is that the way it should be done?
That is the way it should be done. Think of Neutral like a on-off switch regarding power to the rear wheel. Think of Clutch like a dimer or analogical control regarding power to the rear wheel. Think of gears like ........... that is a story for when you have mastered these elementary things ...........