Short answers, pulled from the story.
Robert E. Lee appointed Thomas J. Jackson to organize scattered militia companies sent to Harpers Ferry, Virginia. Jackson formed five infantry regiments and an artillery battery from available volunteers.
Joseph E. Johnston took command on May 15 after replacing Jackson at the post. He expanded the force to include four brigades of infantry and a cavalry regiment led by J. E. B. Stuart.
Johnston and Beauregard merged their commands into the Department of Northern Virginia after the battle. This consolidation marked the end of the Army of the Shenandoah as a distinct entity.
Patterson advanced toward Winchester but stopped after moving only partway because his officers advised caution while some regiments refused to stay longer. These factors convinced Patterson to cancel his advance entirely.
Movement began that evening with each brigade marching to Piedmont where they boarded trains bound for Manassas Junction. Only one train existed on the Manassas Gap Railroad so units arrived sequentially while artillery and cavalry marched overland instead of using rail transport.