Glennon,
You are welcome. This was an interesting case. Please bear in mind that we don't even know if Private Whelan took part in anything that happened after the first paragraph of my last reply, that is, after September 1862. I don't even know if any of the men of the 9th EMM were folded into the 10th or 11th PEMM, much less that he took part in that shipboard mutiny. He may have pitched in to help defend St. Louis when it looked like Price's army would try to steamroll over the city, or he may not have done that. Maybe family letters or diaries and journals would give you more clues.
I should mention that after the fiasco over the 10th and 11th PEMM in St. Louis and the State cancelling most of the PEMM units, the General Assembly appointed a committee that ran an in-depth investigation in early 1864 that found great problems with many aspects of the EMM program. The crux of the issues was that men were forced to enroll in the EMM, and the last Union general to rule over Missouri, MG Granville Dodge, killed the program in March 1865 even before hostilities ended in favor of citizen guards who volunteered and had fewer problems with motivation.

Bruce Nichols