Maybe I can help a little.
Yes Charles Fletcher "Fletch" Taylor did have his own command starting about late June 1864 when he led some of Quantrill's former guerrillas into the Platte County area to provide security to Confederate Colonel John Calhoun Thornton' behind-Union-lines recruiting command then working that area.
Yes, in July he on several occasions worked with John Thrailkill's guerrilla band in combined operations. They did not always see eye to eye on details.
I only know of one severe wound Taylor suffered in the war. This took place August 8 1864 when he was returning to his guerrilla band after attending an area guerrilla council of war evidently in north Lafayette County. While passing through Rush Bottoms, northeast Jackson County, local militia there fired upon his small party severely wounding Taylor in the left arm. A local doctor had to amputate the arm three days later. Some evidence indicates Taylor recovered sufficiently to regain control of his band in September and lead it in operations supporting General Price's great Missouri raid through October 1864. This is from several sources including Yankee ones.
I have not yet seen any account that claims Taylor returned to Missouri later in the war.