Sonata does feel a bit out of place, although it makes a nice intro to Dragon's Den (perhaps live, *wink wink*). I also think it's cool how Church of the Machine just suddenly ends and the listener is confused by the change in tonality from ominous heavy chords to soothing classical. It's unexpected, and I love that.
While I do like Pharaoh at times, I do think it drags on for far too long. Some of the middle section could have been cut (same goes for Smoke and Mirrors and Orion, too). As a whole, though, the song is far better than...
... the Witching Hour. I love the music in this song, but the vocal melodies are just... bad! There's no emotion in the vocals whatsoever; it just seems like Russell is singing a really bad guitar melody. The neoclassical musical sections are great, though, and that one riff in the middle is bad ass.