According to a report by Chief of Ordnance Gorgas, the guns seized at Mount Vernon were:
Over 17,370 unidentified percussion muskets, new and altered (as noted in Gorgas' report, some of these had been removed, so the original total was somewhat more than were then on hand in the arsenal at the time of the count)
20 U.S. Model rifle muskets
2032 Harpers Ferry rifles
33 percussion pistols
0 flint muskets
0 .69 cal. rifled muskets
0 Colt rifles
0 Hall rifles
0 carbines of any pattern
The next item explains where the above arms went (i.e. to the Confederate Government):
EXECUTIVE DEPARTMENT,
Montgomery, Ala., October 7, 1861.
Hon. J. P. BENJAMIN, Acting Secretary of War:
SIR: Your letter of the 19th September was received a day or two since, asking me to aid in arming the regiments composing General Walker’s brigade. It would give me the greatest pleasure to do so if in my power, but it is impossible. I have just armed two regiments at the request of the late Secretary of War, and Brigadier-General Withers notifies me that he needs another regiment, to arm which will exhaust all the State arms. It will be remembered that Alabama transferred to the Confederacy all the arms (20,500) taken at Mount Vernon, and has armed 11,000 troops in the service of the Confederacy, reserving only enough to arm three regiments for State defense.
Very respectfully,
A.B. MOORE
[Governor of Alabama]
The next item explains where some of the arms came from:
ORDNANCE OFFICE,
Washington, D.C., January 15, 1861.
Hon. JOSEPH HOLT,
Secretary of War:
SIR: I have the honor to acknowledge the reference of a letter from the Hon. B. Stanton, chairman of the Committee on Military Affairs of the House of Representatives, asking for the statement of the distribution of arms from the armories to the arsenals and other places of deposit, for safe-keeping, from January 1, 1860. to January 1, 1861, &c., and, in compliance with your directions, have to report that on December .30, 1859, an or(ler was received from the War Department directing the transfer of 115,000 arms from the Springfield Armory and the Watertown and Watervliet Arsenals to different arsenals at the South.
Orders were given, in obedience to these instructions, on January 30,1860, and the arms were removed during the past spring from and to the places as follows, viz:
From Springfield Armory, 65,000 percussion muskets, caliber of .69, and 40,000 muskets, altered from flint to percussion, caliber of .69. From Watertown Arsenal, 6,000 percussion rifles, caliber of .54. From Watervliet Arsenal, 4,000 percussion rifles, caliber of .54. Of which there were sent to Charleston Arsenal, 9,280 percussion muskets, 5,720 altered muskets, and 2,000 rifles; North Carolina Arsenal, 15,480 percussion muskets, 9,520 altered muskets, and 2,000 rifles; Augusta Arsenal, 12,380 percussion muskets. 7,620 altered muskets, and 2,000 rifles; Mount Vernon Arsenal, 9,280 percussion muskets, 5,720 altered muskets, and 2,000 rifles; Baton Rouge Arsenal, 18,580 percussion muskets, 11,420 altered muskets, and 2,000 rifles.
The arms thus transferred, which were at the Charleston Arsenal, the Mount Vernon Arsenal, and the Baton Rouge Arsenal, have been seized by the authorities of the several States of South Carolina, Alabama, and Louisiana, and are no longer in possession of the Ordnance Department. Those stored at Augusta Arsenal and at North Carolina are still in charge of officers of this department.
In addition to the foregoing there have been transfers of arms from the armories to different arsenals, but only in such quantities as the exigencies of the service demand for immediate issues to the Army and to the States, under the act of April 23, 1808, and which I infer are not intended to be embraced in the call of the [?]. Mr. Stanton, whose letter is herewith returned.
Very respectfully, &c.,
H. K. CRAIG,
Colonel of Ordnance.
In addition to these arms at Mt. Vernon Arsenal, there were long arms knowns as "the George Law conversions", which were owned by the State of Alabama, and would have been in the State arsenals (primarily the Montgomery Arsenal).
Additional information regarding what arms were in Federal Arsenals:
"The greater part of the American arms reserve was made up of the .69 caliber smoothbore muskets, a few of them still equipped with flintlocks. The government decided in the mid-1850's to alter all arms to the percussion lock and, in addition, to rifle many of the .69 caliber smoothbore muskets to make them into acceptable rifled muskets. [...]By 1860, most of the flintlocks in Federal arsenals had been altered into percussion locks, with only 23,894 muskets and 652 rifles still unaltered to the new locks. [...It was] reported in November 1859 that the government supply of all rifles and muskets was as follows:
Smoothbore muskets
Altered to percussion, cal. .69 275,744
Altered to Maynard lock, cal. .69 14,765
Made as percussion, cal. .69 213,155
Total 503,664
Rifled Musket
Percussion, since rifled, cal. .69 33,631
Rifled muskets, cal. .58 24,105
Total 57,736
Rifles
Altered to percussion, cal. 54 1,385
Altered to Maynard lock, cal. .54 43,375
Made as percussion, cal. .58 4,102
Total 48,862
Grand Total 610,598"
None of the above manufactured before 1822, and over fifty percent were produced after 1842.
By January 1861, the Grand Total had decreased to 576,800, due to the sale of 11,399 to the States and 31,610 .69 smoothbore muskets to private dealders.
[Source: "Arming the Union: Small Arms in the Union Army" by Carl L. Davis, 1973]
Notice that all smoothbore muskets in the U.S. arsenals in 1859 were .69 caliber. So, even though it is not noted in Gorgas' report, all "17,370 unidentified percussion muskets, new and altered" were .69 caliber.
Gorgas stated that there were no .69 caliber rifled muskets captured at Mt. Vernon. Therefore, most of what was at the arsenal were .69 caliber smoothbores, made between 1822 and 1854 (I think 1854 is when the .54 caliber became the standard). These would have all been various U.S. model muskets.
The "20 U.S. Model rifle muskets" would be the .54 or .58 caliber models.