John Eicher's Civil War High Commands (page 808) contains the rankings. Stonewall was actually sixth in seniority with Longstreet, Edmund Kirby Smith, Leonidas Polk, Theophilus Holmes and William Hardee ahead of him. For the most part the rankings conformed to their seniority as Major Generals, the exceptions being Longstreet, who was jumped ahead of Polk, Holmes and Hardee, and Kirby Smith who was jumped ahead of all of them except Longstreet. In view of Davis' experience with Joseph Johnston when the rank of General was created I suspect Longstreet and Kirby Smith were given a date of rank one day earlier than the others to avoid similar disputes.
Jefferson Davis had written Lee on September 28 informing him of the creation of the rank of Lieutenant General and asking his recommendations for that position in the ANV. Lee unreservedly mentioned Longstreet and Jackson (A. P. Hill was noted as the best of the remaining officers). Lee did qualify his recommendation of Jackson by saying "My opinion of the merits of General Jackson has been greatly enhanced during this expedition." referring to the Maryland Campaign. IMO there was a question in Lee's mind prior to that time because of Jackson's performance in the Seven Days. In addition the Maryland Campaign was the first time the two had worked closely. In the Seven Days and Northern Virginia Campaigns Jackson had operated under Lee's command, but removed from close proximity. Longstreet, in addition to his seniority to Jackson, had been directly under Lee's observation and had performed very well in the Seven Days, Northern Virginia and Maryland. I think the rankings of the two made sense at the time. Regarding the ranking of Polk, Holmes and Hardee, maybe not so much.