Many of the people interested in the history of the 49th Missouri are trying to learn more about the big picture of events happening around the regiment in Missouri during 1864-1865 and during the 1865 Mobile Campaign. I recommend these books that can be purchased at Amazon :
Mobile Bay and the Mobile Campaign: The Last Great Battles of the Civil War : The most recent comprehensive account of the 1865 Mobile Campaign in which the 49th fought.
Price’s Lost Campaign: The 1864 Invasion of Missouri (Shades of Blue & Gray) : This book has the most comprehensive account of the skirmishing near Jefferson City in which the 49th played a role, though their actions are not highlighted in the text.
Inside War: The Guerrilla Conflict in Missouri During the American Civil War : An in-depth examination of guerrilla warfare in Missouri.
Long Road to Liberty: The Odyssey of a German Regiment in the Yankee Army : the 15th Missouri Volunteer Infantry : About 15% of the soldiers of the 49th were born in Germany and this books discusses some of the issues faced by German soldiers in the Civil War.
Civil War on the Western Border, 1854-1865 : Published in 1955, this is an older book but it does provide an easy-to-read overview of the Civil War in Missouri.