track 1 goes at the end.

see?

1) The Strength of the Righteous (tr. 8)
2) Ness and His Family (tr. 9)
3) False Alarm (tr. 10)
4) Death Theme (tr. 4)
5) Al Capone (tr. 2)
6) Victorious (tr. 6)
7) Waiting at the Border (tr. 3)
8) The Untouchables (tr. 11)
9) The Man With the Matches (tr. 7)
10) Four Friends (tr. 12)
11) Machine Gun Lullaby (tr. 13)
12) On the Rooftops (tr. 5)
13) The Untouchables (tr. 1)

"Death Theme" and "Four Friends," whichever version is used, appears in various scenes throughout the film: it presages Costner and Connery's first meeting on the bridge; after "the elevator incident;" Connery's... ; and Costner's office farewell. Likewise, "The Untouchables" (possibly both versions) and "Victorious" are spotted in various scenes, sometimes just for a few seconds.

"Ness and His Family" and "Al Capone" are also edited for separate scenes ("Ness" maybe making 2-3 appearances, the same for "Capone"). And "On the Rooftops" receives repetitious edits in the film, extending its 2:33 album length by a few mintues at least.

Most of the cues are edited in the final film, with some passages (on the album) not even in it.

Hope this helps.

1) The Strength of the Righteous (tr. 8) - The Main Title
2) Ness and His Family (tr. 9) - As we see Ness reading the news about the little girl death
3) False Alarm (tr. 10) - just before the attack on the warehouse
4) Al Capone (tr. 2) - the long hotel traveling, ending on Capone's bed
5) Victorious (tr. 6) - Malone leads Ness to a sucess attack on Capone's booze house
6) Waiting at the Border (tr. 3) - prior to their assault on the Canadian border
7) The Untouchables (tr. 11) - the assault on the Canadian border (first time we hear the triumphant Untouchables theme)
8) Death Theme (tr. 4) - first hearing on Charles Martin Smith's death scene on the elevator, played again on Connery's death scene
9) The Man With the Matches (tr. 7) - the long traveling around Malone's place, ending with the break in
10) Machine Gun Lullaby (tr. 13) - the train station sequence
11) On the Rooftops (tr. 5) - Ness chases the gangster
12) Four Friends (tr. 12) - Ness bids farewell to Andy Garcia
13) The Untouchables (tr. 1) - the end title

Yes, some cues are used again slightly different in other scenes, but this are I think the correct order as we hear on the CD.

As for why Morricone sequences his albums the way he does, I can't explain. Never read anything about it. But I think he likes to think on his albums as musical experience, not worrying about correct track sequences etc. But who knows for sure?