"The Constitution does not give the federal govrnment the authority to tell states how to fill vacancies in their legislatures. And since the Federal government should be working with local authorities to combat rebellion, then it should make every effort to identify and recognize those authorities. Since much of the Virginia legislature were ringleaders in that rebellion Congress recognized those who didn't and allowed them to partition the state."
Let me take care of this in reverse. Regarding the non-highlighted portion - there is nothing in the Constitution that supports your theory. In fact Lincoln himself argued that the majority of revolutionaries had the right to supress the minority.
Now, if I remember correctly, the Full Faith & Credit Clause REQUIRES the federal and state governments to recognize the acts and proceedings of a state government - as long as that action meets the prescribed guidelines laid down by the federal government. I think I even traced the history of that legislation with another poster (#3Fan if memory serves.) Once the states affixed their stamp of approval - state seal and entry into legislative records - the acts were official. Congress could not rewrite the rules of acceptance since that would violate the prohibition against ex post facto legislation.
ex parte Milligan (9-0 decision) reinforced the idea that the Constituion CANNOT be suspended - even in time of war or rebellion. That being the case - any recogonition of any other state legislature would be unconstitutional and void. Your whole argument (seccession is illegal) mandates that the states were still states - and the federal government has to recognize the legislatures of those states. But if you agree that the states had legally seceded, then the federal government can recognize whomever they want since they are no longer a state.
Your choice. WV admission was unconstitutional, or the secessions were legal and Lincoln invaded a sovereign country - a war of Northern Agression. You decide.
In the first palce I don't think that the the Full Faith & Credit Clause has the meaning you thought it had. Article IV, Section 1 says:
Full Faith and Credit shall be given in each State to the public Acts, Records, and judicial Proceedings of every other State. And the Congress may by general Laws prescribe the Manner in which such Acts, Records and Proceedings shall be proved, and the Effect thereof.
That requires each state to recognize the ations of another state. But since Virginia was in rebellion, and the leaders who had been elected were the ringleaders of that rebellion, then under the second sentence then Congress might actually have the power to determine if the proceedings leading to the creation of the reformed Virginia legislature were legal and base it's recognition on that.
Your broad interpetation of Ex Parte Milligan is as irrelevant as it is inaccurate. The Constitution wasn't suspended, far from it. The requirements in Article IV, Section 3 were followed. The question isn't if the actions of Congress were constitutional since they clearly were. The question is if the reformed Virginia legislature was legal and I haven't seen anything that indicates that they were not. If you can cite which laws were broken then I would like to hear them.