When you get right down to it, in creating West Virginia Congress didn't do anything unconstitutional, either. They received a petition from the recognized legislature of Virginia and acted on it, all in accordance with Article III, Section 3. Their actions were legal and constitutional.
No, Double D, what you need to show is that the reorganized legislature of Virginia was illegal. You need to provide evidence that, in light of the fact that the rest of Virginia was in rebellion and did not consider itself part of the United States, the act of loyal citizens forming a legislature loyal to the federal government violated some law. Show what law was broken then and maybe you will have a case. No opinions, please, just cite the relevant code. If you can do that then maybe you'll bring me over to your position.
"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.