I'm pretty sure that you're misinformed about Libby being a Clinton holdover. Google around and you'll see.
Libby held Undersecretary positions in the DOD in the middle 1990s, policy and strategy and resources. No idea if they require Senate confirmation. He was also lawyer for a key Clinton ally, Marc Rich. Was Rich one of the pardoned in Clinton's last week in office?
As far as the holdovers, Bush kept nearly all of Clinton's federal prosecutors. Clinton fired all of them and replaced them with his people. That's for starters.