I am assuming that the Michael Muldoon who served in company D is the same person as the Michael E Muldoon who served in company H. Note, however, that the only direct evidence in favor of that is the Pennsylvania Archives card on the company H Muldoon. Further, the index to compiled service records has separate cards for them.
He was born in 1843/44 (3 (19, muster rolls have '34', in 1861), 7 (17 in 1861)).
When he enlisted, he was living in Philadelphia (7).
He enlisted and was mustered into service, in Philadelphia, Pennsylvania, on 25 September 1861 or 20 December 1861 (1 [20 Dec], 3 [25 Sep], 4 [25 Sep], 7 [25 Sep]). He was mustered in as a private, in company D (1, 3, 7, 8, 9 (co. H)).
He was transferred to company H.
According to the company D records, he deserted on 25 October 1861 (1 [unknown date], 2, 3 [unknown date]). He was discharged at Philadelphia, Pennsylvania, on writ of habeas corpus, probably because he was a minor (4, 5, 6, 7). He was a private (8 (co.D), 9 (co. H)).
1 Bates, Samuel Penniman. History of Pennsylvania volunteers, 1861-5. Harrisburg: B. Singerly, state printer, 1869-71. 5 volumes. 'Ninety-first regiment', volume 3, pages 186-233. (In the roster) (Michael Muldoon [co.D])
2 company D, register of deserters (Michel Muldoon)
3 Civil War Veterans' Card File, available at the Pennsylvania State Archives, searched 9 August 2004 (Michael Muldoon [co.D])
4 Bates, Samuel Penniman. History of Pennsylvania volunteers, 1861-5. Harrisburg: B. Singerly, state printer, 1869-71. 5 volumes. 'Ninety-first regiment', volume 3, pages 186-233. (In the roster) (Michael E Muldoon [co.H])
5 company H, register of men discharged, #2 (Michael E Muldoon)
6 company H, descriptive roll, #23 (Michael E Muldoon)
7 Civil War Veterans' Card File, available at the Pennsylvania State Archives, searched 5 March 2005 (Michael E Muldoon [co.H])
8 index to compiled service records of volunteer Union soldiers who served in organizations from the state of Pennsylvania (Michael Muldoon)
9 index to compiled service records of volunteer Union soldiers who served in organizations from the state of Pennsylvania (Michael E Muldoon)