Below is a list of resources I have found on historical doctrinal issues in church music, separated into major categories of discussion.
Psalms-Only vs. "Hymns of Human Composure"
Bonner, David Findley. The Psalmody Question. Middletown, N.Y.: Hanford and Horton, 1908. http://www.archive.org/stream/psalmodyquestion00bonn#page/n3/mode/2up
Cotton, John. Singing of Psalmes a Gospel Ordinance. London, 1647. http://www.archive.org/stream/singingofpsalmes00cott#page/n5/mode/2up
Freeman, Frederick. Psalmodia, Or, The Pastor's Plea for Sacred Psalmody. Philadelphia: J. Whetham, 1836. http://www.archive.org/stream/psalmodiaorpast00freegoog#page/n6/mode/2up
Latta, James. A Discourse on Psalmody. Philadelphia: William W. Woodward, 1794. http://www.archive.org/stream/discourseonpsalm00latt#page/n5/mode/2up
Mant, Richard. Thoughts on the Singing of Unauthorised Hymns. London: Rivington, 1835. http://www.archive.org/stream/thoughtsonsingi00mantgoog#page/n4/mode/2up
McMaster, Gilbert. An Apology for the Book of Psalms. Philadelphia: Daniels & Smith, 1852. http://www.archive.org/stream/apologyforbookof00mcma#page/n5/mode/2up
McNaugher, John. The Psalms in Worship. Pittsburgh: United Presbyterian Board of Publication, 1907. http://www.archive.org/stream/psalmsinworships00mcna#page/n5/mode/2up
Morton, George. Review of Dr. Pressly on Psalmody. Pittsburgh: Luke Loomis, 1850. http://www.archive.org/stream/reviewofdrpressl00mort
Pressly, John Taylor. Review of Ralston's Inquiry into the Propriety of Using an Evangelical Psalmody in the Worship of God. Allegheny, Penn.: John B. Kennedy, 1848. http://www.archive.org/stream/reviewofralstons00pres#page/n3/mode/2up
Ralston, Samuel. Defence of an Inquiry into the Propriety of Using an Evangelical Psalmody in the Worship of God : Against the Objections of Rev. John T. Pressly, D.D. Pittsburgh: George Parkin, 1844. http://www.archive.org/stream/defenceofinquiry00rals#page/n5/mode/2up
The True Psalmody: Or, the Bible Psalms the Church's Only Manual of Praise. 2nd ed. Philadelphia: William S. Young, 1859. http://www.archive.org/stream/truepsalmodyorbi00phil#page/n7/mode/2up
A Cappella Singing vs. Instrumental Accompaniment
Briney, John Benton. Instrumental Music in Christian Worship. Cincinnati: Standard, 1914. http://www.archive.org/stream/instrumentalmusi00brin#page/n7/mode/2up
Dodwell, Henry, and John Newte. A Treatise Concerning the Lawfulness of Instrumental Musick in Holy Offices. London: William Hawes, 1700. http://www.archive.org/stream/treatiseconcerni00dodw#page/n13/mode/2up
Girardeau, John Lafayette. Instrumental Music in the Public Worship of the Church. Richmond, Va.: Whittet & Shepperson, 1888. http://www.archive.org/stream/instrumentalmus00giragoog#page/n8/mode/2up
Glasgow, James. Heart and voice: instrumental music in Christian worship not divinely authorised. Belfast: Aitchison & Cleeland, n.d.
http://books.google.com/books?id=XG4DAAAAQAAJ
Hancock, Tyre. Church Error; or, Instrumental Music Condemned. Dallas, Texas: Tyre Hancock, 1902.
http://books.google.com/books?id=mucsAAAAYAAJ
Instrumental Music in Christian Praise. Toronto: James Bain, 1880. http://www.archive.org/stream/albertatest_01205#page/n3/mode/2up
McGarvey, J. W., and Amos Sutton Hayden. "Instrumental music in churches." Millennial Harbinger, Nov. 1864-May 1865. https://sites.google.com/site/davidsscriptorium/home/mcgarvey-hayden (An audio version is available at: http://www.archive.org/details/McGarvey_Hayden_Instrumental_Music.)
McGarvey, J. W., and Frank Gibbs Allen. What Shall We Do about the Organ? Nashville, Tenn.: McQuiddy, 1903. http://www.bible.acu.edu/crs/doc/mcal.htm (An audio version is available at: http://www.archive.org/details/McGarvey_Allen_Organ.)
The Organ Question Critically Examined. 2nd ed. London, Ontario: Free Press, 1884. http://www.archive.org/stream/cihm_45894#page/n3/mode/2up
Peirce, James. A Tractate on Church Music. London: S.n., 1786. http://www.archive.org/stream/tractateonchurch00peir#page/n7/mode/2up
Proceedings of the Convention of United Presbyterians Opposed to Instrumental Music in the Worship of God. Pittsburgh: Myers, Shinkle & Co., 1883.
http://books.google.com/books?id=ue0sAAAAYAAJ
Robertson, John. Memorial and Complaint. Toronto: S.n., 1859. http://www.archive.org/stream/cihm_35837#page/n7/mode/2up
Robinson, Alexander. Instrumental music: a discussion of the question, Is there divine authority for the use of instrumental music in the worship of the New testament Church? Belfast: Witness Steam-Printing Works, 1883.
http://books.google.com/books?id=qvdEAAAAYAAJ
Congregational vs. Choral
Conversations on the Choral Service: An Examination of Popular Prejudices against Church Music. London: Thomas Harrison, 1853. http://www.archive.org/stream/anapologyforchu00hodggoog#page/n2/mode/2up
Diagnosis of Non-Congregational Church Music. S.l.: S.n., 1865. http://www.archive.org/stream/diagnosisnoncon00diaggoog#page/n8/mode/2up
General and Miscellaneous
Gibson, James. The Public Worship of God: Its Authority and Modes, Hymns and Hymn Books. London: Nisbet, 1869. http://www.archive.org/stream/thepublicworship00gibsuoft#page/n3/mode/2up
Hodges, Edward. An Apology for Church Music and Music Festivals. London: Rivington's, 1834. http://www.archive.org/stream/anapologyforchu00hodggoog#page/n2/mode/2up
Norris, E. J., and E. G. P. Wyatt. A Plea for Retaining the Gregorian Chant. Wantage: Convent of S. Mary, 1909. http://www.archive.org/stream/pleaforretaining00norruoft#page/n3/mode/2up
