I agree that some of the transitions (or lack thereof) give the song a very jerky feeling, but overall I can say I enjoyed most of this song, especially the solo and everything afterwards.
I think this song could use a little bit of trimming/re-arranging, since some parts such as the aforementioned portion at around 1:10 and the death-metal style tremolo picked portion shortly after don't seem to quite gel with the rest of it. I can only guess the reasoning behind some of these parts is to sound much more progressive and shake up the rhythm and time signatures a bit, but there's a time when you should do that and a time when you shouldn't.
I love the intro and solos however, and that one little "marching" section at 2:29 is pretty cool too.