Can I run just one wire to the sub-panel via schedule 40 separate from the others?
Run a new feeder in metal conduit

If you're going to run a conduit from the main panel to the subpanel, I would simply run a 2" EMT and pull an entirely new 100A feeder (1AWG Al hot/hot/neutral with the EMT for a ground) through it in your situation.  This is because the existing feeder SE(?) cable seems to have been improperly installed to begin with (its jacket does not extend down into the strain-relief clamp on the cable entrance), and as a result should not be relied upon for continued service.

While you are at it, you should re-terminate the existing NM cables into junction boxes above the panel, then bring the circuits down from those boxes using NM "jumbo pigtails" into the panel that are properly strain-relieved.  This because the original installer screwed up the strain relief on the branch-circuit NM cables going out of the subpanel, as well.