George, I searched on two primary themes. The Catholic religion and the term "Prayers for the President". I got many hits. I only posted the tip of a larger collection of information. I left out...

1. Several Catholic Churches burned.
2. The shooting of a priest who required amputation of his legs
3. The looting of valuable religious artifacts from a Catholic Church near St.Augustine Florida.
4. The arrest of several priest.
5. The conscription of monks from a Benedictine Monastery into the army.
6. Threats of church closings that did not pray for the United States President.

Now usually these type of things are shared between North and South, in this case I only found one of the above instances not related to the Union Army, a Catholic church burning in Missouri, but these were guerillas and not regular forces so at this point it looks to be a Union effort to supress the Catholics. I found too a letter to Lincoln, in early 1865 warning him to be aware of Catholic assassins. But it is not transcribed

http://memory.loc.gov/cgi-bin/query/P?mal:1:./temp/~ammem_uEri::

The Prayer for the President.

This is a part of the war I never knew and this revelation has effected me more than anything has in the history of this war. It's one thing to lose a war but to be forced to give the gift of prayer, the sacred act of communication with the devine spirit, to the man responsible for the deaths of their sons and husbands, is subjugation of the worst kind. This is the act of a monarch, king, or emperor. This changes a lot about what I've thought about this war.

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David Upton