What restrictions does the state and federal power over militias necessitate on freedom of association, speech, or right to keep and bear arms
Arguing that this man has the right to run around and play soldier in the woods due to the freedom of association and RKBA is a different argument than claiming this man is part of the original militia as envisioned by the Founders. Which argument are you making?
As to restrictions, at the very least, I would argue that giving the State the sole authority to appoint officers of the militia and authority to train is a meaningless provision of the Constitution if any random guy can create his own opposing militia. Under the definition you propose, MS-13, the Crips and Bloods are as much militias as any random group of men in Arkansas.
The Founders also wrote in provisions in the Constitution to suspend habeas corpus in the even of rebellion. Their discussions in the federalist papers clearly show they appreciate the practical problems of allowing bands of armed warlords to form outside the authority of the democratically elected governments. Shays Rebellion happened in 1787 after all...
Second, you are quoting the section that descrbes the unorganized militia. This is not the organized militia which trains, drills, and is subordinate to the state. The unorganized militia is the pool from which the organized militia is formed. The unorganized militia has an individual right to keep and bear arms apart from the organized militia precisely so it can be a source of that pool.
This does not mean though that the select elements of the unorganized militia get to
organize, create their own independent structure, select their own officers and establish an organized militia independent of the state. States may allow such behavior (and Arkansas may be one of those states); but it isn't a right protected by the federal Constitution.
Finally, let's look at some of the state constitutions of the original 13 colonies....
North Carolina: [T]he people have a right to bear arms, for the defence of the State; and, as standing armies, in time of peace, are dangerous to liberty, they ought not to be kept up; and
that the military should be kept under strict subordination to, and governed by, the civil power (1776).
Pennsylvania: That the people have a right to bear arms for the defence of themselves and the state; and as standing armies in the time of peace are dangerous to liberty, they ought not to be kept up; And
that the military should be kept under strict subordination, to, and governed by, the civil power (1776).
Vermont: [T]he people have a right to bear arms for the defence of themselves and the State -- and as standing armies in time of peace are dangerous to liberty, they ought not to be kept up; and
that the military should be kept under strict subordination to and governed by the civil power (1777).
Virginia: That a well regulated militia, composed of the body of the people, trained to arms, is the proper, natural, and safe defense of a free state; that standing armies, in time of peace, should be avoided as dangerous to liberty; and
that in all cases the military should be under strict subordination to, and governed by, the civil power.
So how do you propose that the military should remain in strict subordination to civil power if private citizens have an unlimited right (through freedom of association and RKBA) to organize as separate militias unauthorized by the state or civil power?