Well, this is what I came up with, including pretty much everything you've already spotted - if I'm forgetting something, feel free to tell me.
I named each theme/motif/progression, so it might be easier for me to remember and refer to those pieces being repeated somewhere else. So, for instance, the chord progression which opens the album is set to an organ, so I called it "Dark organ progression". Or, there is this bit (you'll know which one) which is sung first by Nafaryus, but mostly by her daughter, so I refer to it as "Faythe's theme".
If the original poster or any of you would prefer to copy/paste whatever you want from this, no problem at all. In fact, with this sort of threads, I think it would be cool to have some sort of 'collaborative', wikipedia-ish file, so that anyone gets a chance to add something.
Also, I couldn't find any recurring theme or motif for some songs (like "The Gift Of Music" or "Whispers On The Wind"), which I think is weird. Maybe some of you can help me?
Anyway, here is Act 1:
1. Descent Of The NOMACs2. Dystopian Overture0:00 A. Dark organ progression (Im-II-IVm-V)
0:22 B. Nafaryus’ theme
0:44 C. Arhys’ theme
1:13 D. Heaven’s Cove’s theme
1:45 E. Sword fight motif
2:03 F. Frenetic 11/8 motif (à la 1:36 in “Surrender To Reason”)
2:28 G. Faythe’s theme
2:56 H. Brothers’ theme
3:25 I. Playful motif
3:46 J. Daryus’ theme
4:00 K. Gabriel’s theme
3. The Gift Of Music4. The Answer0:00 L. The Answer intro
0:25 M. The Answer verse (by Gabriel)
1:14 N. The Answer chorus (by Gabriel)
5. A Better Life4:07 D. Heaven's Cove theme (guitar and strings)
4:23 %. Better Life motif (by Arhys over strings)
6. Lord Nafaryus0:00 B. Nafaryus’ theme (by Nafaryus)
0:30 O. Tango motif
0:59 P. Short piano break
2:23 G. Faythe’s theme (by Nafaryus)
2:52 G. Faythe’s theme (minor key; by Nafaryus)
7. A Savior In The Square0:00 Q. Savior motif
1:18 P. Short piano break (guitar; end of solo)
1:49 R. Royal motif (by Nafaryus)
2:53 R. Royal motif (by Gabriel)
3:44 G. Faythe’s theme (by Gabriel)
8. When Your Time Has Come0:00 L. The Answer intro
0:35 S. WYTHC verse (by Gabriel)
1:20 T. WYTHC chorus (by Gabriel)
3:21 U. Moment motif (by Faythe)
9. Act Of Faythe0:00 K. Gabriel’s theme
1:06 G. Faythe’s theme (by Faythe)
2:23 T. WYTHC chorus (chord progression only)
3:57 R. Royal motif
10. Three Days0:14 A. Dark organ progression (by Nafaryus over piano)
0:18 +. Evil progression (by Nafaryus over piano) (Im-IIb-V-VIIm)
0:55 V. Gadget riff (by Nafaryus)
1:11 ~. Baroque progression (by Nafaryus) (IVm-VII-III-Im)
1:28 W. Bow-down motif (by Imperial Guards)
2:47 W. Bow-down motif (by narrator)
11. The Hovering Sojourn12. Brother, Can You Hear Me?1:27 H. Brothers’ theme (by Arhys)
3:05 X. Revolution theme (by Gabriel)
3:59 H. Brothers’ theme (by Gabriel)
13. A Life Left Behind4:40 Y. Sinister motif (by Arabelle over strings)
14. Ravenskill2:22 K. Gabriel’s theme (minor key)
4:12 U. Moment motif (by Faythe)
4:55 Z. Chosen verse (choir)
5:47 Six Degrees Of Inner Turbulence
15. Chosen0:30 Z. Chosen verse (by Gabriel)
1:28 @. Reason motif (by Gabriel)
16. A Tempting Offer0:39 J. Daryus’ theme (by Daryus)
1:19 W. Bow-down motif (à la 2:47 in “Three Days”)
1:51 Y. Sinister motif (by Arhys/Daryus)
2:31 $. Offer motif (by Daryus)
3:19 J. Daryus’ theme (by Daryus)
3:44 Y. Sinister motif
17. Digital Discord18. The X Aspect1:38 C. Arhys’ theme (major key; by Arhys)
2:22 C. Arhys’ theme (by Arhys)
3:16 %. Better Life motif (by Arhys over strings)
3:28 H. Brothers’ theme (bagpipes)
19. A New Beginning0:54 I. Playful motif (by Faythe)
1:10 B. Nafaryus’ theme (by Nafaryus)
1:45 I. Playful motif (by Faythe/Arabelle)
2:00 A. Dark organ progression (by Nafaryus over organ)
2:18 ~. Baroque progression (orchestra)
3:32 I. Playful motif (by Faythe/Nafaryus)
5:15 +. Evil progression (guitar)
5:32 A. Dark organ progression (guitar)
20. The Road To Revolution1:19 G. Faythe’s theme (minor key; by Faythe)
1:49 G. Faythe’s theme (by Gabriel)
2:20 G. Faythe’s theme (chord progression only; by Daryus)
2:34 X. Revolution theme (by Arhys)
3:05 W. Bow-down motif (by Nafaryus; à la 2:47 in “Three Days”)