Earlier quoted context omitted.
No, it was because the slave states didn't want to lose slavery in a Senate vote. If you think CA is too populous for it's people deserve an equal vote, CA should be 6 states. But the slavers fought that too (Missouri Compromise). State boundaries are legal constructs inherited from obsolete aristocracy, not meaningful cultural boundaries. It makes no sense to solve a hypothetical tyranny of large states by replacing…
No, the Several States are the Sovereigns. They ceded a small amount of authority to the Federal government in a limited Federal Constitution that outlines the powers of the Federal government. See the 10th Amendment.
That ended at Appomattox and with the ensuing Civil War Amendments - see the 14th Amendment.