I think that Harper's Ferry was the center of gravity. I think General Jackson would agree.
Destroy the B&O and the Chesapeake and Ohio canal. Dig in on the Blue Ridge like crazy, heavy artillery, the works. Artillery could cover all the way down river to the bend about to where dam #3 is today. Make the Federals attack across the Shenandoah and then uphill. Fortify the Short Hill Mountain ridge as a fallback position. Put a chain across the Potomac upstream of the Shenandoah confluence with batteries to cover it. Don't know the railroad situation to the south in early '61, but build them up for sure.
Would not have been easy, the Federals knew full well what was at stake. Put Lee in charge of the defense (he was brilliant in positional fortified war, think the Siege of Richmond) with Jackson as the maneuver element, and, as Patton put it, "grab them by the nose and kick them in the (rear end)."
Joe Johnston downstream on the Potomac line. Put Bragg out to pasture. Have Forrest raid into Indiana and Ohio and burn Cincinnati. Don't shell Sumpter, no military or Naval reason for it, and a huge mistake.
Davis was a nice guy, dutiful to a fault, etc., but not the man for the job. In hindsight Forrest was.
Not an armchair general, have bigger ambitions than that! Armchair geostrategist (and history buff), at your service!
Reading Mary Chesnut's Civil War diary. This is not verbatim but from memory as it's a few chapters back:
The angels came down to retrieve Stonewall Jackson's soul but couldn't find him, they return to heaven crying but there he was... He he had flanked them and gone in the gates ahead of them!