What happens if you are concealed with misdirect and then run a stormtrooper through with a lightsaber. Does the misdirect drop? Does it only drop for the guy stabbed?

I'd say that Misdirect would drop if the person being attacked was the same person you targeted with Misdirect. Kind of hard to ignore a person when that person is attacking you directly and has inflicted a nasty injury.

Of course, if you'd used the Magnitude Upgrade, then those additional targets would still be subject to Misdirect's effects.

I would say, that "not until get harmed". I know that when Ventress attacked Dooku was imbued by a "magic ichor" but, they only became revealed when Dooku used Unleash on the group.

Someone using Sense or Seek (Seek so probably) can see through the illusion and ignore penalties (they became "hidden" for the rest unless the Seek user).