So, I cleared all of the security from level 1. Opened up the "blocked by security" room, and found 2x sparq beams with no magnum pistol. Am I missing something? Used the sparq to clear out the corpses and crates. No magnum to be found.

that sounds like the armory

the one for the magnum is further along behind a secret door
specifically use the 2nd door in the same hallway as the armory
follow along this path until you get to a large very irregular room
the secret door is at the bottom of the stairs that lead up to the
radiation trench with the puzzle to activate a red forcebridge
in the secret room it should be laying on the floor with 3 emp grenades


i hope this helps ya find it