"Here We Are Juggernaut", "The Broken", "When Skeletons Live", "Made Out Of Nothing", "Guns Of Summer", "World Of Lines".... I dunno, I've got a good deal of songs off that album I love.
I think the production is mostly what was initially so jarring about that album. The songs sound more traditionally Coheed when played live.
Digging: Boy Hits Car - All That Led Us Here