I could live without the two Portnoy songs, which would reduce the album length down to under 48 minutes, which would have made it a perfect album (slightly shorter than Maiden's Powerslave).
I would rank the songs as follows:
1. Stream of Consciousness
2. In the Name of God
3. As I Am
4. Endless Sacrifice
5. Vacant
6/7. This Dying Soul and Honor Thy Father
By the way, it's not that I dislike the Portnoy songs, but both songs have that angry young white guy vibe that I don't really care for and (for me) don't really have anything memorable about them. The other five songs, on the other hand, are diverse, well-written and contain myriad memorable riffs/hooks, etc. As I Am comes close in tone to the two Portnoy songs but has memorable and clever songwriting elements and does the "fast and loud" thing much better. Endless Sacrifice is a really strong "poppish" DT song. Nothing great about Vacant, but it's cool for what it is, and the use of the cello is very cool. Depending on the day, Stream of Consciousness might be my favorite DT instrumental (although the Beatles/Crimson sections drag a bit for my taste). ItNoG puts it all together, and the embedded nuggets are a cool touch.