I was under the impression the intended double album would be arranged the way MP did on the FII Demos Ytse Jam release.
Anyway, I really dig the idea of opening with TOT. Yes, it's got the slow intro, but once it takes off, the energy just skyrockets, and I find the whole thing incredibly compelling. Following with the ballad single is interesting, as is ending with Hk/LITS – I'm sorta ignoring AL as I agree with several other posters that it doesn't work (on the album, at all).
This is the one I put together, with a way different approach that will likely be disliked equally:
Burning My Soul
Just Let Me Breathe (great transition from BMS, though, with some crossfading)
You Not Me (w/extended opening and ending from demo)
Peruvian Skies
Hollow Years
Lines in the Sand
The Way It Used to Be
Take Away My Pain
New Millennium
Hell's Kitchen
Trial of Tears