Does Christ's ruling in the millennium mean the Father and the Spirit are set aside?
No. Christ's millennial rule does not set aside the Father or the Spirit. Although Christ reigns during the thousand-year Kingdom, the rest of the Godhead remains in the background and is not canceled. God is a triune Spirit Godhead, so the triune Godhead remains.
Les explains that even though Christ rules and reigns, especially over the thousand-year Kingdom reign, the rest of the Godhead is still sort of sitting back in the background. We cannot forget that or cancel out God the Father and God the Spirit. When dealing with God, we are dealing with the triune Spirit Godhead, and Les does not want to lose that truth. He then transitions to Ephesians for further study.
For he hath put all things under his feet. But when he saith all things are put under him, it is manifest that he is excepted, which did put all things under him.