I mean no disrespect, but I am having difficulty with some of your points. Perhaps you are using sources unknown to me. I know you have read and studied a lot about the Civil War in southwest Missouri, and perhaps you have not done much about the war in west-central Missouri.
I understand that Colonel John Trousdale Coffee was not the easiest commander to work with based on Colonel Jackman's memoirs, mentions of Coffee's drinking and court martial in the "Official Records, and his refusal to convert his Missouri State Guard unit to Confederate regular service in early 1862." I mean no insult to your family or to Colonel Coffee, but Colonel Coffee had his own distinctive reputation, and seemed to work hard to perpetuate it. However, I have not read anywhere else that Colonel Coffee refused to work with Quantrill's guerrillas. Perhaps some of the regular Confederate recruiters in the Lone Jack campaign were reluctant to soldier with the guerrillas, but I have not before seen any reference to those soldiers refusing to work with these irregulars. In fact, Quantrill's men provided security just a few weeks earlier in July for Colonel Upton Hays' recruiting command in this same area, and with his band fought alongside the regulars at the Battle of Independence on 11 August just a few days before the Lone Jack battle on 16 August.
To the contrary, memoirs and other accounts I have read imply Quantrill and his men enjoyed a good working relationship with the large Confederate recruiting cadre then working in the Jackson County area. In fact, Colonel Gideon Thompson between the two battles mustered in William Quantrill as a captain and several of his men in lesser leadership ranks into the partisan ranger service. This is widely known from several sources including guerrilla memoirs. This is the only certain commission or promotion that we can assert with confidence for Quantrill from reliable sources.
I was not aware that General Hindman had any effect convincing the Confederate legislature back in Richmond to pass the Partisan Ranger Act in April 1862. Hindman was not named commander of the Trans-Mississippi West until May 1862, but I cannot account for his whereabouts in April. I know that he received his promotion to major general in April, though. Where did you obtain the information that he helped implement the Partisan Ranger Act? Maybe I missed that one.
Of course, you are quite correct that the Federals did not recognize the legitimacy of partisan rangers as legal combatants, as evidenced by the large numbers of them that they executed in Missouri.
Would you please share your sources for some of the information that you mentioned.