What is the ruling on money acquired through embezzlement and theft under a government that does not uphold Allah's law, and what should I do with it after repentance?

You must offer sincere repentance for all sins, by abandoning them, regretting them, and resolving not to return to them. As for the money you stole from the state, you must return it to the state treasury if they are just in its collection and distribution. Otherwise, you should spend it on general Muslim welfare, such as bridges, mosques, and road infrastructure, or give it as charity to the poor.