Sorry for the late reply, busy holidays and all that.
Anyway, when it comes to those dissonances, it's most likely due to the tubular bells. At every arpeggiated triad (A7 and Gmaj7 both with omitted 3rds) all of the instruments are playing notes that are from the triad, so while theoretically it's supposed to not clash, it's probably the timbres causing the issue.
As far as the timpani and horn, I completely understand what you mean. They're not totally sequenced perfectly, and I'm currently looking for a way to deal with it. The timpani being mechanical bothers me to an extent where I feel like reworking the intro, especially because I feel like I can't just jump into the tune like the original does. I'm not really satisfied with the intro anyway, it was an idea, but every time I look back to it I'm not that thrilled with it.
2:14 is the slentam ringing out, which is something I actually wanted. The bleeding is also why I tried spacing things out. As for the higher pitches, I'm not completely certain, but I think that's the tubular bells.
When it comes to the structure, nothing's set in stone, and I was going to expand the section around 2:10, fix the intro, and vary the repeat at the end. The ending itself was a cop out so I'm most likely going to finish that too.
Thanks for all the feedback.