Here's what I've come up with.
(Set 1 ~ 78:00)
The Root of All Evil
I Walk Beside You
Another Won
The Killing Hand (2004 extended version)
Another Day
The Mirror (Demo Version with "Lie" middle part) 10:15
Raise The Knife
The Spirit Carries On (with extended intro)
Finally Free
(Static plays through the intermission)
(Set 2 ~ 71:00)
The Glass Prison
This Dying Soul
Vacant (segue into) (with cellist)
The Answer Lies Within (with strings)
Sacrificed Sons (with full orchestra)
Octavarium (with full orchestra)
(Encore ~ 11:00)
Metropolis (with full orchestra)
Total length (without intermission) = 160 minutes, or 2 hours and 40 minutes, so definitely shorter than 3 hours, and not too much longer than the actual Score CD set (which reads as 2:37:09 in my files).
I liked what you had with the first four songs, but I felt like "Another Day" would be a good cool-down after TKH and before "The Mirror", which I would've liked to see them play the demo version, which includes an instrumental that would later become "Lie", and maybe fill that part with some wicked solos between Jordan and John. "Raise The Knife" stays as is, and while it might be a bit of a cheat to include two songs from SFAM, I couldn't resist putting both TSCO *and* FF, because I've always wanted to see them play FF to close the first set and let the static play through intermission.
Then of course, you'd open with TGP, and who couldn't resist putting TGP/TDS together. Though after 25 minutes of non-stop metal barrage, it would be time to come down a bit, and I thought it'd be neat to slowly introduce the orchestra, with just some members playing "Vacant" and then "The Answer Lies Within", then the full orchestra for "Sacrificed Sons" and "Octavarium" as they did on the actual Score concert. And then of course, "Metropolis" remains as the encore. Honestly, if I wanted, I could've also thrown in another 8VM track, but both sets were around 70-ish minutes already and I didn't want to make them feel unbalanced.
-Marc.