Interesting question you pose.
In 2006 the team fell apart in the second half because the pitching went south but also because the hitting stopped driving in runs with men on base and in key situations. I'd submit (and this is just my opinion) that the 2006 team "only" hit home runs, they lost that balance they had in 2005. Like subsequent Sox teams when they didn't hit home runs, coupled with less than stellar pitching in the second half, they lost games, period.
This was the result of the Thome for Rowand deal which changed the overall dynamic of the club. (That's not saying ANYTHING bad towards Jim, a true professional by the way) The Sox became a softball-like, station to station team.
When you look back I'm surprised Kenny did this since it was his bold decision to change the dynamic of the team with the Lee / Posednik deal before 2005 that helped that club win a World Series.
Kenny felt he was improving the team and again he gets credit for having the guts to make the move, it just didn't work out as well as what he did the year earlier.