To what category do popular sovereignty, limited government, federalism, republicanism, individual rights, separation of powers, and checks and balances belong?

All of them are Principles of Government.

Individual rights are unalienable rights that are guaranteed to all citizens.

Popular sovereignty means that the authority of the government comes from the people that elect their representatives.

Separation of Powers is a separation of responsibility and limitations that are given to each branch. The system of check and balances is also a part of this, giving each branch a way to limit other branch and control it.

Federalism is a system of government that divides the power into national and state governments.