1. None that bother me personally.
2. This is just personal preference, but made me leave the vocal out of the intro part to a make it seem more like an intro that's building to something. Would make the vocals that come later be more impactful maybe.
3. You could experiment with a more "epic" sounding organ that matches more with the tone of the song. A big, sinister cathedral organ type. Not on expert on organs so can't be more specific.
4/5. For this I'll just refer to the mix as a whole. You need to EQ the backing instruments so they interfere less with the lead guitar and vocals. Just cut a bit at the frequencies where the lead and vocals sit. During times when both the vocals and lead play at the same time (2:36), you probably need to use to to automated EQ to temporarily have the lead guitar duck out of the way of the vocals. That way the vocals can still be clear with out having them stick out.