Ditto on the tuning issues.  Be sure everyone is using the same tuning standard and actually tunes their instruments before a take.
 
Vox is also off pitch in a few places... or it might just be the way it sounds with that guitar out of tune in the background. Listen to the vocal note held at 1:50. 
 
Guitar solo's need to be in the same key and use the same scale as the song's melody. There's a lot of missing passing tones in the solos.
 
It has a Dylan feel to it. Could be a very cool song when the issues get fixed.

Great song - love the harmonies.
Definitely the tuning issues that everyone else mentions.
If you are using an NI Kontakt organ, it could be the organ - I have had the issue myself - one of the updates took care of it.

Thank you all, guys!  we appreciate your feedback so much!
 
daryl and rik who asked about whether or not the organ was the thing out of tune - no, it's not the organ.  I did play some dissonant notes but everything I played is in the key and they're on pitch.  I'm using a real Hammond XK3c audio output not a softsynth or sampled organ so it's good.
 
but we are working on the problems we have found due to your feedback!  thanks again!

Yep...as Reece has stated, we are going to re-track several of the guitar rhythm tracks, just to be on the safe side.  
 
I know that Sean is taking another run at the main Solo in the middle of the song.  I am going to rework my Outro Solo.  I guess no one appreciates Jazz any more.     
 
I am going to leave the song up for now, but will post a new mix when I have everything together.  

I too mostly noticed intonation - not to pile on, but you might want to tighten it all up tuning wise. 
 
The panning of guitar material seemed a bit arbitrary, too, though I'm no one to talk about that kind of thing. 

I have posted a new mix for this song, follow the same link above. This version has two new electric rhythm guitar tracks. Also, the middle Solo in the Outro solo have been redone.

Hope this sounds better.

This is much better.  I really like this tune, and I love your rendition of it.  You do know that Bob Dylan recorded a trio of christian themed albums right after he was saved:
 
https://en.wikipedia.org/wiki/Saved_(album)
 
The albums are actually very good, but were never mainstream.  I'm sure you probably knew about these, but I thought i'd throw that reminder out there.  Does your band play any of these?  (your song is very much in this style).

michaelhanson
I have posted a new mix for this song, follow the same link above. This version has two new electric rhythm guitar tracks. Also, the middle Solo in the Outro solo have been redone.

Hope this sounds better.

Much better!

Much better... Yep, the instruments are sounding good. 
 
I would still run some Melodyne on the lead vox to get rid of the quaver in the singing and tune them just a bit in a few places where the vocal drifts off pitch.  You don't need to run it to the 100% level..... just fix the obvious nits.There's no shame in using ME to tame a few things. I use it on every vocal that comes through my studio. Some need it more than others but I still use it to look at the vocals to see what's happening in them.
 
And.... I would bump the vocals up a few dB since it is really difficult to pick out the lyrics with the vox setting so far back into the mix like it is now.
 
Getting closer to a finished mix.

David- Thanks for listening again and commenting.  Your suggestions made a noticeable difference to this song.  
 
I did know about Dylan's Christian based albums from the past.  One of my good college buds was a huge Dylan fan and had every album that he ever released.  I have not listened to them in a while.  Scandalous Grace has never attempted to cover one, we have elected to do all of our own songs.  You can check most of them out on my sight. As a group, we trade off on Lead Vocals.  The main writer of the song, usually takes the Lead.  
 
James- Super happy this one sounds much better to you.
 
Herb- Glad you think the instrumentation sounds better.  I have no Melodyne phobia here.  I have had the program since long before it came with Sonar.  Let's say, that sometimes I make artistic decisions on when to leave some character in a song.  I know that bothers some folks, but I have always felt that "perfect" is not always better.  Reece had mentioned some "wavering" to me.  I told him that I sang it that way on purpose.  Now, if I was grossly out of tune, I would re-sing the phrase, or "fix" it.