It is legal in all 50 states to organize a militia, it is illegal in all 50 states to do certain things as a militia including (the exact rules vary by state) things like participating in civil disorder, planning to participate in civil disorder, training for sabotage or guerilla warfare, etc.

Of course, since the purpose being suggested here is literally the purported urgent need to engage in armed rebellion against federal authorities, the concern that organizing a militia for that purpose would be constrained by merely "organizing a militia" being illegal is a bit odd. Waging war against the federal government, or conspiring to do so, is--even if one argues that it is morally justified by the government violating its Constitutional constraints--both clearly illegal and likely to be subject to the absolute maximum sanction. The legality of organizing a militia in general hardly makes a difference, either to the legal or practical risk anyone undertaking such a venture would face.

I know what study you are reading and the case it uses to argue that is highly flawed.

This is basically what Ammon Bundy did, and most of the US hates him for it. The federal government tried many times to jail him but ultimately he was found innocent everytime. Finally they managed to get him by a friendly judge who had a husband high up in the BLM, awarding an ungodly high lawsuit when he helped an innocent mother get her baby back by summonsing his protest-militia to protest a hospital that conspired to have the baby taken by child services.

Seriously, listen to some videos of Ammon Bundy actually speak (he is pro immigration rights as well, despite the 'far-right' label). Not what you hear from the media or others or under the influence of a political agenda. Most of what he says is 99% in line with your thought process here.