Anddrsonh1,
I think your original impression was the correct one. The list of his unforced failures is long -- a few:
1. Though he knew all winter that his position at Centreville, Va was not tenable, he retreated toward Richmond with so little regard to a plan that a huge amount of precious meat was lost at the Thoroughfare Gap meat plant and much Manassas Gap RR rolling stock was isolated on the western end of the road, which Johnston knew could not be held.
Johnston remained at Centerville because he was waiting for the Confederate Government to decide if it could get him some reinforcement so he could attack into the North. He only ever considered the position temporary and a staging point for an offensive at that, it was entirely unsuitable as a defensive positon.
Furthermore objected officially to the establishment of the meat packing plant at Thoroughfare Gap - correctly arguing that it was a tactically exposed position. His objections were completely disregarded.
The official records stated that of the 2,706,733 pounds of pork and beef at Thoroughfare only 369,819 pounds were left behind after the withdrawal, and of that 200,000 pounds was given away to local farmers.
2. Battle of Seven Pines was poorly run.
No more so than Lee's first major offensive at Mechanicsville. A general can hardly be condemned for his first attempt at a major offensive battle involving tens of thousands of troops going awry.
3. Knowing that he had to work with Pemberton to survive against Grant, he none-the-less did little until Pemberton was closed up in Vicksburg. Then it was too late to be effective.
He arrived at Jackson on May 13th, two thirds of Grant's army fell upon him the next day driving him from the city, then his plans for the campaign were betrayed to his enemy when a courier took written orders from him for Pemberton to McPherson who sent it to Grant. Grant then having full knowledge of the intentions of his enemy acted upon it and struck while they were still seperate. After being driven from Jackson, Johnston was a day or so behind events until Pemberton was besieged.
He had arrived mid-campaign with no up-to-date information on the campaign - and what little he was given was inaccurate - and was almost immediately set upon by the main body his enemies forces then betrayed and his plans handed to his enemy. What General, exactly, could have been successful in those circumstances?
4. Though pressed repeatedly to rescue the precious, and plentiful, rolling stock of the Mississippi railroads after Vicksburg fell, he never managed to get the bridged across the Pearle River completed so the locomotives and cars could be saved.
Johnston ordered the bridge rebuilt. The work lagged but was that his fault or the inadequecies of the Confederate Engineers?
5. He came within a hair's breadth of loosing his entire army in northern Georgia by letting a Union army get in his rear. He knew of the danger and the passes that had to be protected, but did not take sufficient measures to defend them. Only the timidity of the Union general prevented the loss of his army.
He did not have the man power to defend every pass through the mountain, he did not know where all of his enemies forces were, and his cavalry commander was not scouting as he was daily being directed to do. Johnston placed his main forces in the areas he thought most likely to be attacked. He was wrong, but that didn't make his decision unreasonable nor unjustified. When the Federals came through Snake Creek Gap he deployed the entirity of Hood's Corps to meet it and prepared to move his whole army if the threat was serious enough - only halting the move when Hood cautioned him that the advance through Snake Creek Gap might be a diversion following McPherson's aborted advance on Resaca.
What did he do right? He let Beauregard fight the battle at 1st Manassas, he fought hard to supply his troops in all situations, and........
Johnston took control of 1st Manassas.
He allowed Beauregard to prepare and plan it because he felt Beauregard would know the area better as that's where his army had been, but Beauregard's plans only reached one of his subordinates before the federals attacked and made them obsolete. Beauregard ignored the fighting on his left flank and claimed it was only a fient. For most of the morning he stood idle on Lookout Hill waiting for the chance to launch his own offensive, while Johnston stood in the background reluctant to step in because of his delicate sensibilities for proper military ettiquette.
Johnston was the man responsible for sending Jackson, Bee, and Hampton to the left to reinforce the threatened sector, and when finally he could stand the inaction no longer and was fed up with his suggestions that the battle was actually happening on the left getting dismissed, Johsnton announce "The battle is there. I am going" and left Lookout Hill to head to the left flank to take control, leaving Beauregard to follow in his wake.
Johnston and Beauregard rallied the troops - Johnston even being the man to send Bee to the troops he said that famous "there stands Jackson like a stone wall" comment to - then it was Johnston who fell to the rear to establish an Army HQ to control the battle, to find reinforcement and get them to the to front, and then to send Kirby Smith and Early's Brigades on the flank attack that won the day.
Beauregard, meanwhile, was riding up and down the front shouting encouragement to the men and replacing fallen officers with his own staff. He too ordered an offensive, only after the flank attack which won the battle had been launched.
If any one general could have claimed to have been resonsible for winning 1st Manassas then Johnston had a more legitimate claim there than Beaureard - especially when you add in the fact that if Johnston hadn't been so prompt in bringing his army out of the Valley to support Beauregard's then it's likely the Federals would have won that battle.