Yes, they were sovereign. Their sovereign status was recognized in the 1783 Treaty of Paris. Madison described them as sovereign in the federalist papers. The SCOTUS has affirmed their sovereign status many times. It’s not in question.
Congress is not empowered to determine the status of a state.
Several previous presidents held that unilateral secession was perfectly constitutional. Thomas Jefferson and several others openly and repeatedly said so.
Do you have sources for any of those claims?
As far as I am aware the only Supreme Court case dealing with secession is Texas vs White (1869) and it was determined that secession was unconstitutional. That is a fact and settled law.