I wouldn't worry about seeing 5V at the Kreg terminals, especially if you can dial in the 6C45P plate voltage as expected. Your heater voltage is 6V, so there's nothing to address there.
You may find that the 12AU7 needs a few days of running in to awaken and reach full emission, and that these Kreg voltages may creep up a bit as that particular tube gets some more run time.