Very interesting piece. Military school issue is a possible answer, but we will likely never know why the gun was shortened, it is possible that it was fired with a muzzle blockage (dirt or a tampion) and the muzzle bulged or even split. When turned in to an armorer, it was shortened by 3 or so inches to keep it in service. Or, it was possible that the musket was surplussed with the damaged muzzle from such an accident and the new civilian owner shortened it.
As far as it being a "2nd or 3rd class weapon" after percussion was adopted, remember that the flintlock was a front line issue for both sides at the beginning of the American Civil War. The Battles at Philippi and Manassass and other early engagements saw troops of both armies using them, often the majority of soldiers in line of battle. The Confederate military was still issuing flints as late as mid-1862 to Stonewall Jackson's troops during the Shenandoah Valley campaign, over a year after the beginning of hostilities and it wouldn't surprise me to find that rear echelon Federals were using them mid-war as well. And, a flint musket hammer was excavated from the Confederate lines at the battlefield of Sailor's Creek.