Something seem to annoy me; I can't tell you where, but I have the impression that you have a string that keeps ringing continuously, check the linked notes where you cross from one key to another. I might be wrong though, if it's so, it might be because of a dissonnance created by the presence of a harmony in minor scale that wasn't there in your previous version.
Nice song dude. Reminded me a bit of The KillJoy by Insomnium http://www.youtube.com/watch?v=2Aj_ka8rLf0
Also, The section that starts at bar 95 is in 3/4. That's why it looks pretty messy in 4/4.
it could be the light strings hanging out at the end, or the guitar at the breakdown, but I'm having trouble locating the problem note, and that part should be in 3/4 lol, I'll change that today