Okay, mage is infiltrating the building, and astral guard sees him and manifest to tell him to stop.

Mage goes astral to fry to poor son of a bitch. This takes a simple action. Now he wants to Stun ball him, how is the resolved. Does he have to wait till the next pass? or can he start to cast it, but the guard gets a simple action first?

He has to wait.

He would need to wait, unless he somehow manages to surprise the guard. Doing something to not get killed until his turn might be a good idea, though.

Thanks, I tried to compromise by allowing him to cast at the same time as the other mage. He still smoked the sucker.

Security mage manifests speaks.
Pass #1:
Security mage holds action?
Runner mage astrally perceives.
Security mage takes action to return fully to the astral.
Pass #2:
Security Mage uses astral init
Runner Mage uses meat body init.

Manifesting was a stupid decision. The security mage should have sent a messenger watcher and held action, then when the runner mage perceives he blasts him on the same pass.

You are correct. This will not happen again, lol.

Also, new question, do sustaining modifiers affect drain tests, or resistance (damage or magical) tests? Need to know.

Nope!

Although the wageMage made a tactial error, the runner made an even bigger one, he should have burnt Edge to ensure that he'd go first after popping into the Astral.

Really? I though that because Drain tests was not a damage resistance test Sustaining did modify the test.

Fair enough, Wasn't completely certain that this was just SR4.

In SR3 and before the opposite was true...