Granted, you already know there are some overall level issues with the guitar, so I won't discuss those. I noticed where the initial lead guitar part comes in at around 13 seconds, you have the lead and rythm panned hard left right. I think that is creating too much separation between the tracks so they come across as somewhat disjointed if that's even the right word I'm trying to use... Probably not.
at around 40 seconds, where you have the clean tone arpeggiated guitar (which I really dig btw) it sounds like you could bring up the highs or high-mids just a bit on that arpeggiated part. Same for the other times that part enters within the song.
You know, now that I have listened to the whole song (sorry I'm typing while listening), I feel like you should use a distortion with different characteristics for that one lead guitar throughout the song. It sound too hi gain for the application (merely, my personal opinion based on my listenging tastes). Have you tried using a more bluesy tube overdrive type soudn for that? Could make things a lot different. Maybe some verb or a delay or something too. Nothing big and overbearing, just maybe a little extra texture for that part of the track. Maybe better, maybe worse, just my .02
