OK. Attacking the supply line was one option I posed. Pemberton himself thought that it was an option as well. He surely, despite his faults, would have appreciated the difficulty of living off the land and the psychology on the troops of being completely dependant on food in a foreign land. I'm aware Grant took ammunition with him, but forcing him to fight means he needed more than he carried and therefore reliance on the roads to Port Gibson. The wounded were transported to Port Gibson, but the conditions were less than ideal even for the time, hence McClernand taking his with him.
Grant did fight and use ammo: he won battles at Raymond (May 12), Jackson (May14), Champion Hill (May 16) and Big Black River Bridge (May 17). The Confederates could have fought bigger battles or more battles to make him use more ammo -- but if they were going to keep losing them all the way they got handled in those, they might have been even worse off.
Taking your wounded with you when you are on a movement like Grant's is pretty common: the only real alternative is to leave them behind to be surrendered to the enemy, and people generally don't like that. Cavalry raiders would do it at times, or armies forced to retreat.
I wouldn't rate Pemberton's thinking processes too high. He does not show well in uncertain situations or when faced with surprises. Grant had served with him in Mexico and had a low opinion of his ability.
However, normally there would be no problem with attacking an enemy's supply line as Pemberton suggested or as you do. The difficulty is that Grant had no intention of relying on one, preferring freedom of movement, and that Grant had learned by personal experience a few months earlier that there was a lot of food to be gathered in Mississippi if you sent armed soldiers to get it. So if Pemberton moves as that plan demands, Grant doesn't care much: it will cost the Confederacy Vicksburg and free up the Mississippi River. Grant will simply ignore them and move directly on Vicksburg.
The assault on Grants supply line aside, what do you suppose was the possibility of Johnston defending Jackson or at least putting up a stiff fight?
Low. Johnston has about 6,000 troops; Grant is closing with close to 30,000. Johnston has about 4000 troops scheduled to arrive late on May 14, another 4,000 on the morning of May 15 -- but Grant is already there on May 14, pushing in Johnston's defenses. Staying would be a bold gamble quite likely to turn into bloody defeat.
Moving northwest to pose a threat to Grants right and closer to Pemberton while culling together reinforcements?
This puts Johnston in a bad position for joining up with his own reinforcements that are headed for Jackson. Grant might decide to hit any one of these forces then, concentrating against them and crushing small parts in detail. It also puts Johnston in a bad position for maintaining his own LOC, and might end with Johnston himself trapped in Vicksburg if things went really bad.
More reinforcements from Bragg sooner?
Johnston had been with Bragg's Army immediately before this. He knew very well what reinforcements might be expected and how fast they might arrive from Bragg. The answer comes down to "not much". Rosecrans was well-aware of what was going on and could be expected to strike if Bragg detached more troops (as Rosecrans had done at Murfreesborough when Bragg detached troops to transfer to Pemberton in December 1862). In fact, Halleck and Grant grew very frustrated with Rosecrans in May-June of 1863 precisely because Rosecrans was waiting for the perfect moment to launch the Tullahoma Campaign (Rosecrans spies were watching Bragg carefully, hoping to see him detach more troops as part of that). Washington wanted him to attack to keep Bragg pinned.
Actually entering the area of operations sooner and taking control?
I'm not sure he could have been. Johnston had been ordered to the AoT because of the political squabbling up there, to possibly relieve Bragg. Bragg's wife was sick when he got there, so Johnston wouldn't send him off to Richmond. When she was better, Johnston seems to have had a bad period from his Seven Pines wound and was bed-stricken for a bit.
Appreciating the importance of not just Vicksburg, but the entire Mississippi from Vicksburg to Port Hudson?
I think that was appreciated, but the Confederate command structure was all wrong for it.
Johnston a) believed Davis was setting him up as a scapegoat for anything that went wrong; b) wanted an army command, not a theatre command and c) believed the authority was wrong. He thought both sides of the river at Vicksburg needed to be under one command, and that Bragg's AoT should not be part of that command.
More cavalry in Mississippi?
In late January, Van Dorn's command was transferred to Bragg, which is why Pemberton was so short on cavalry. By mid-February, Van Dorn was up there, effectively commanding Jackson's division and Forrest's brigade and a bit more (maybe 7,000 cavalry), while Wheeler commanded the other half of Bragg's cavalry to the west.
This was done because the Confederates were falling in love with the cavalry raid. In December, the combined effect of Van Dorn's Holly Springs raid and Forrest's raid into West TN had stopped Grant dead in his tracks in northern MS. Van Dorn took out Grant's advance supply depot; Forrest ripped up 60 miles of RR and telegraph, cutting Grant off from Memphis just as Sherman was downriver getting smashed at Chickasaw Bluffs.
That convinced the Confederates that a major cavalry concentration in TN would threaten the flank of and prevent any advance overland from TN towards Jackson/Vicksburg. It certainly was a problem for Grant, as his LOC would have stretched as he went south, requiring more and more detachments against cavalry raids.
Pemberton, not surprisingly, wanted his cavalry back and couldn't get it. That's why Grierson's Raid worked out.
Tim