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In my decades of reading about the Civil War I have never seen any reference to Lee having over 90,000 troops (including Jackson's recently arrived command) at the beginning of the Seven Days.
Long ago I transcribed appendix 2c of Harsh's Confederate Tide Rising. Here it is:
"In his memoirs, Joseph Johnston referred to Lee's forces on June 26 as "the largest Confederate army that ever fought." He estimated Lee's reinforcements as follows: 15,000 from North Carolina, 22,000 from South Carolina and Georgia and 16,000 from Jackson, for a total of 53,000. When combined with the 73,000 Johnston had on May 31, this would have given Lee 126,000 men. Johnston later admitted his figures were too high. For example, he counted Lawton twice (with Jackson and with Georgia); he included forces that did not arrive until July and August; and he overestimated Holmes by 150%.
Johnston's claims affronted that plank of the "Lost Cause" myth that insisted the Confederates had always been heavily outnumbered, and his figures were emphatically rejected by Charles Marshal, Jubal Early, Jefferson Davies, the Reverend J. William Jones, and Walter Taylor, who insisted Lee had 80,000 men or fewer. These defenders of Confederate meagreness indulged in a bad habit of mixing apples and oranges." They used the figure for their own "effectives", a stripped down statistic, whilst employing "present for duty" figures for the enemy. Their 80,000 may be fairly effective for Lee's combat effectives, but then it should be compared to the approximately 70,000 McClellan had in the same category.
The total of 112,220 present for duty for the Army of Northern Virginia…. Breaks down as follows:
Attacking Column North of the Chickahominy
Army of Northern Virginia
Longstreet: 14,291
A.P. Hill: 16,411
D.H. Hill: 12,318
Stuart: 2,109
Total: 45,129
Army of the Valley
Jackson: 9,604
Ewell: 6,353
Whiting: 5,537
Cavalry: 605
Total: 22,099
Confederate defensive forces south of the Chickahominy:
McLaws: 4,915
D.R. Jones: 4,503
Magruder: 5,671
Huger: 6,160
Holmes: 9,018
Reserve artillery: 1,680
Cavalry: 2,000
Richmond defenses: 9,136
Petersburg defenses: 1,909
Total: 44,992 "
Note that Lee left ca. 45,000 men manning the defenses, and this must be taken into account. 45,000 men in permanent works is not the sort of thing you can just waltz over. McClellan himself on the 26th sent inquiries to his corps commanders about the strength south of the Chickahominy, and all replied they could see no dimutation of strength, correctly as the forces Lee shifted north were not manning the defences, but were behind Richmond.
Even more interesting is Steven Newton's Joseph E. Johnston and the Defence of Richmond. He estimates Johnston had 72,739 PFD on the Peninsula, and on 1st June had 94,813 PFD before deducting the Seven Pines casualties, excluding the Richmond defences etc.
The Confederates were much stronger than is usually supposed.