I don't think the content of the story is actually mixed up timewise like that. The band's first album, Second Stage Turbine Blade, is the story's second chapter. The new album is the fourth chapter. Well, part 1 of the fourth chatper. After they finish up chapter four, the plan is to go back and do chapter one. So they have two more albums of story left to go.
As far as the actual content of the story, it's not a very clear narrative. I own the two comic books they've put out so far, which takes things up through "Everything Evil," track 4 of SSTB. The comics make the story marginally clearer, but still, the lyrics are pretty tough as far as figuring things out. I think Claudio also has a bunch of musical cues that are supposed to represent certain things, but he hasn't done a lot of explaining about what each cue is supposed to mean.
Mostly I like the band for the excellent two-guitar interplay, catchy melodies, and the way they have one foot planted in the punk world and one in the 70's prog world.