Oddly enough, for such a naturally cautious man, McClellan seemed insensitive to the risks he ran. On May 26 a storm drenched both armies, turned the roads into bottomless pits of mud, and threatened to wash away the few bridges spanning the Chickahominy. "Richmond papers urge Johnston to attack, now [that] he has us away from the gunboats," McClellan wired Stanton, appending calmly: "I think he is too able for that." This would have been an astounding conviction coming from any general whose divisions straddled a flood-swollen river in the presence of an undefeated enemy, but from McClellan it beggars belief. How could McClellan, who has gone down in history for his ability to overestimate the size of Confederate armies, have been so sanguine in his belief that Johnston was "too able" a general to attack an army divided into non-supporting fragments?
The explanation is painfully simple: what McClellan told his superiors he believed is not what he really thought. The general did not, in his own calculations, credit Johnston with nearly twice his own numbers. He was not misled by Allan Pinkerton (alias Major E. J. Allen) feeding him inflated estimates of Rebel troop strength which were accepted as if carved in stone. On the contrary, McClellan had very good intelligence which eh [sic] used quite cynically to prod the Lincoln administration for reinforcements.
"Little Mac's" spurious accounting began with his own strength reports. He kept his official record of his numbers low by a variety of devices: omitting officers and discounting troops available for front line duty but temporarily on special duty were his two mainstays. McClellan managed to maintain the fiction throughout April and May that his army usually contained less than 100,000 men. Of these he contended fewer than 89,000 were infantry carrying muskets into the line of battle. As biographer Stephen Sears has pointed out, "there was nothing really wrong with this way, except" and these were very large exceptions, "his obstinate refusal to explain what he was doing" and the fact "he was guilty of deliberate slight-of-hand by not counting the enemy army the same way he counted his own."
[Indeed McClellan did take his combat strength excluding officers and minus 1/6th of his infantry etc. who were detached to the logistics - if one uses McClellan's 20th May '62 return one finds 91,346 men PFD in the infantry corps, cavalry reserve and advance guard - the fighting part of the army. Converted to combat effectives this would yield a force of ca. 76,000, approximate parity or perhaps even moderately outnumbered by the enemy army. Newton is thus in error in suggesting McClellan was excluding officers etc., but he is parroting Sears. Sears is equally incorrect, but parroting an article by Irwin in Battles and Leaders (link) - Irwin compares McClellan's statement of numbers of combatants with the aggregate present of all units including non-combat units. McClellan was not stripping down "duty men" in his claim, but using the PFD of his combat units.
Also Lincoln at this point started a dialogue with McClellan where he started using McClellan's "aggregate present and absent", which is also the strength category many authors use for McClellan's movement onto the Peninsula. By this measure McClellan had 128,864 officers and men, including non-combatants and those physically absent; Johnston has a similar number in this category being 125,143 the month before, excluding reinforcements received.]
Union intelligence officers made their guesses of Confederate strength by penetrating the commissary department of Johnston's army. This resulting in two distinct pieces of data: numbers of regiments and numbers of troops. In both cases, Pinkerton's estimates were far more accurate than has heretofore been admitted. He asserted on May 3 and again on June 26 that Johnston's army at Yorktown contained "the following-named organization: Twenty-two brigades, ninety-one regiments, three legions, two battalions infantry, five battalions artillery, sixteen companies artillery, and two companies infantry," which amounted to 100-120,000 men. "Now the only trouble with this," contended historian Bruce Catton, "was that Johnston at the time had barely 50,000 men on the peninsula," and that assertion, butressed by Douglas Southall Freeman, Clifford Dowdey and others, has left a lasting impression that Pinkerton's reports were purely flights of fancy.
In fact, Pinkerton had been uncannily accurate. While Johnston's own reports are confusing enough to make it difficult to separate his artillery out into battalions, the detective got everything else correct. Within three days of Pinkerton's first estimate, Johnston reported that his army possessed twenty-two brigades of infantry and cavalry (exactly Pinkerton's estimate), ninety-three regiments of infantry, cavalry or militia (against an estimate of ninety-one) and seven independent infantry or cavalry formations (again, exactly the estimate).
So, granting that Pinkerton got the organization of the Confederate army almost perfect, how did he manage to inflate the Rebel troops from Johnston's stated estimate of 55,633 to more than 100,000? In actuality he did nothing of the sort. Johnston's report involved the same kind of ersatz numbers as did McClellan's. [sic, see my comments above] He desired reinforcements as badly as his counterpart, and distrusted his superiors almost as much. So Johnston sent all his reports to Richmond in "effectives," which represented only the total available armed enlisted strength of the army, not the ration strength or "aggregate present" that Pinkerton was counting. Worse still, it can be easily shown that Johnston undercounted even those. At the end of May, Johnston's army contained at least 72,239 officers and men "Present for Duty." But "Present for Duty" strength was still far less than "Aggregate Present" which included soldiers in hospitals, under arrest, and detailed to non-combatant jobs [only "extra duty", not "special duty"]. Pinkerton himself alluded to this, when he cautioned McClellan that, while Southern regiments were organized with 1,000 men, "the regiments will not average over 700...." Despite everything McClellan wrote his superiors, he knew that Johnston's army in [sic] the peninsula could not have exceeded 75,000 officers and men, if measured in the fashion he calculated his own strength.