He only issued Order 66 after the Windu fight, he wouldn't have had the chance to before he was killed. And even if he did transfer his consciousness, he'd basically have to start over from scratch in politics since he wouldn't have any of the political pull he had.
It's a clone body, so as long as he gets on the holocommunicator fast he can still issue the order, I say he could do it inside of a minute. As for the politics, he still controlled the Seperatist/Trade Federation Army, and if he neutralised the republic army, which he supplied in the first place ironically, then he could still conquer the republic. After that it's just consolidating his power. Really all that would have changed is his anti-alien policies, which would have focused on specific species rather than a "if you're not human you're scum" agenda.