I believe I gathered these tidbits from Behind Enemy Lines- Sidney Jackman

Denied his general's star, Coffee left his Regt, & Gideon Thompson succeeded him as its cdg officer. Thompson's new command consisted of only three Co’s of Cav & one Co of Infy. After Coffee's resignation, official reports afford scant information about him until Price reorganized the army in the summer of 1864. Shelby received command of a division composed of his Bgde & those of Jackman & Col Charles H. Tyler. Coffee, in turn, became the Col of a "paper" Regt of Missouri Cav, transferred from Jackman's Bgde to Tyler. Coffee's orders gave him until Sept 1 to fill his Regts’ ranks.

Following Jefferson Davis's proclamation forgiving deserters, Coffee believed that hundreds of deserters, located in the northern tier of Ark counties, would return to CS ranks. Coffee & Jackman & over fifty other officers were empowered to recruit. (80) Shelby thought that 3,000 men might come in, & if this occurred, Coffee again would have a full Regt to command. However, the recruiting success did not materialize; & when Shelby prepared to join Price in his 1864 raid of Missouri, the Cav cdr debated whether to leave Coffee at Batesville, Ark, to continue recruiting, or to take him along. He decided that leaving Coffee would only provide "a nucleus for the deserters to come back to." Since this was undesirable, he order Coffee to join Jackman's Bgde in the expedition & allowed him to recruit to fill his Regt beyond the Sept 1 deadline. (81) Coffee thus recruited & the expedition traveled to Fredericktown, Missouri; he hoped to fill his quota of men, but, by Oct 3, he had not done so. Shelby relieved Coffee from Jackman's Bgde & ordered him to report to Price.

8/19/64 Shelby to Col Jackman cdg Bgde-you were ordered to consolidate the 2 Co’s of Coffee’s Regt or send the extra Co to Col Schnable. This has not been complied with-a Regt is allowed only 10 Co’s and it can’t be organized with 11 Co’s and any election of officers thereby voided. These tricks will not be tolerated.

10/2/64 Shelby orders II. Col John T. Coffee, Jackman's Bgde, is hereby relieved from duty with Jackman's Bgde, & will report with his Regt to Maj-Gen Price at once

After the Battle of Westport, in late 1864 or early 1865, Coffee moved his family overland to Waco, Texas. A family history suggests that Coffee went to Waco at the invitation of friends of his brother, Franklin Brown Coffee, who had been a member of the Texas Rangers. (83) While the reason for his trip may never be known, his staying in Missouri could have been disastrous.

Passed over as senior Col in Price's army, Coffee had lost the coveted brigadier's star. The Drake Constitution of 1865, adopted by the Missouri State Convention, debarred him from practicing law & holding political office in Missouri, both of which he had pursued as his peacetime livelihoods. Death had claimed his third wife in late 1863, leaving him to care for seven children, five of them under fifteen years of age. Discouraged, apprehensive, & worn out from four years of fierce warfare, Coffee, with his children, joined scores of Missouri Confederates who decided to start a life anew in Texas