How do I set my guns to heavy stun?

You can't.

If this is the mission I think it is, it happens automatically. Fire at whatever makes you happy.

Correct. Its the Everything Old is New Again mission. Its just part of the dialog to set weapons to heavy stun, but you don't have to do anything to have that happen.

I actually brought along a phaser just for the mission, thinking I needed to stun lol. Turns out the mission just bugged on me and I couldn't get through that part. No trouble 2nd time through, just used a regular weapon and fired like normal.

I tend to think that unless specificly mentioned, weapons are allways set on stun.

Why?

Because every single enemy you take down can be revived if they have a medic nearby.

even "vaporized guys" can get rezzed, which to me is really odd.

Combat Medics can bring back a vaporized person? I know "vaporized" is merely an animation and then a invisibility flag applied to the body, but there also needs to be a "can't be revived" flag as well.

Maybe they use section 31's trick and beam the person out a split second before the beam hits, like Sloan did on Romulus. :p

The weirdest bug involving "dead" npcs I've seen was in Cutting the Cord, the last of the Cloaked Intention Series.

SPOILER IN INVISO-TEXT:

At the end while you're fighting Hakeev, Obisek and his buddies beam in and Obisek gives a little speech. At that part, just before Obisek beamed in, a thalaron drone dropped a mine right in the middle of everything. The mission goes to the cut scene where Obisek is giving his speech, the mine goes off and melts all the Remans. They disappear and the fight continues. I finally defeat Hakeev and afterwards Obisek climbs out of the ground along with his men, all looking like melted zombies, and continue the mission like it never happened.

/SPOILER

I was laughing so hard I almost choked.