There is only one version of this instrumental.
The track duration differs on the various CDs, but that is merely due to where the track splits were defined between Prelude and You Can't Take Away The Lord.
On We Wish You A Larry Christmas it is a cleaned up vinyl, or possibly cassette transfer.
Upon This Rock (Capitol)
Upon This Rock (Radio Promo CD, 1998)
Upon This Rock (Illegal Noise Series CD, 2001, titled "Upon This Rock" on the artwork)
We Wish You A Larry Christmas, CD 1998
The Prelude was created to emulate the excitement of a Broadway musical, previewing the melodies which would become familiar over the duration of the play. Upon repeated listenings it would also effect the listener in another way, reminding them of what songs were coming up and letting them fill in the lyrics and identify the songs as they became more and more familiar with the music. It was also a way of changing the rock experience to a more disciplined presentation instead of simply ten random songs collected together.