Where exactly does Meade claim to have had only 9,000 men present on the 17th?
These are the numbers he gave, and are quoted in Carman.
Carman estimates:
1st Corps: 8,619 inf and 819 art
2nd Corps: 15,206 inf and 859 art
5th Corps: 1,684 inf (only the five reg bns that crossed the creek) and 1,540 art (inc. arty res)
6th Corps: 1,684 inf (Irwin's bde only) and 901 art
9th Corps: 11,714 inf and 979 art
12th Corps: 7,239 inf and 392 art
Cavalry: 4,320 PFD (including regiments not present and the horse artillery)
Carman does not estimate for the 4 unengaged regular battalions, Morell's division of 3 bdes or the 5 brigades of 6th Corps that did not make an attack.
The 4 regular battalions of Lovell's brigade are 1,040 on the 20th, and this is a good estimate of the unengaged portion.
The PFD of Morell is 5,409, which is obviously more than effectives.
In B&L Franklin estimated his 5 brigades engaged at South Mountain at 6,500 effectives, and they took slightly 533 casualties, and so they have ca. 6,000 effectives. The missing brigade is Hancocks, with a PFD of 2,114.
Thus Carman gives 55,946 engaged. To this we can add:
4 regular battalions: 1,040*
Morell's division: less than 5,409*
5 of Franklin's brigades: + 6,500+2,114*-533-1684 = 6,397
(* note these are PFD and thus an overestimate of effectives)
Unengaged but present = 12,846
Total = 68,792
Now this is likely too high, but should be viewed as the maximum number of effectives McClellan had on the field. A few thousand should be knocked off for the non-effectives in Morell's div and Hancock's bde. Moreover, some of the numbers Carman reports he admits are the PFD, as no estimate of effectives was available. Where there was no available data he used the largest available figures for the Federals, and thus is overestimating a bit.
Take the case of the 132nd Pennsylvania. The colonel reported he took 750 men into action, but that evening they only had 364 present after taking 152 casualties. This implies that the effective strength of the regiment was 516, and that a third of those claimed to be in action were not.