Wow! Let me see if this very interesting thread that's on life support can be revived. I would have voted that Patterson was made the scapegoat, and quickly. While he does deserve some responsibility for not preventing Johnston from re-enforcing Beauregard, Patterson was given conflicting and confusing orders by Scott. By July 12th Scott appeared unconcerned about Johnston moving to Manassas. When one of Scott's staffers reminded Scott that McDowell expected Johnston be kept at Winchester Scott sent the following disingenuous order to Patterson on the 13th: see Williams, Lincoln Finds A General, p. 81
"I telegraphed to you yesterday, if not strong enough to beat the enemy early next week, make demonstrations so as to detain him in the valley of Winchester; but if retreats in force towards Manassas, and it be too hazardous to follow him, then consider the route via key's Ferry, Leesburg, etc."
Here's an order than contains three if's; thus violating the age old principle of military orders: Keep it simple. This order was also a fine example of Moltke's axiom "If an order can be misunderstood, it will be misunderstood." Besides the lack of simplicity it was also a bad order. By following Johnston through Leesburg, Johnston would have arrived at Manassas three or four days earlier than Patterson, as Johnston had the use of the railroad from Strasburg, while Patterson could not use the railroad from Leesburg to Alexandria as the rail line had been torn up and rolling stock destroyed.
Scott's order should have been specific. If he wanted Johnston to remain at Winchester, he should have said so and annulled all previous orders to Patterson, except for the one permitting Patterson to change his base of operations to Harpers Ferry. The fact that Patterson was a nobody, and Scott was a very big somebody, the potential of loosing Scott at this juncture in time was too big a risk, McDowell was the only general with experience in commanding large number of troops, so Patterson was the logical sacrifice.