Here is a catalog of comparison between The Phantom Menace special edition DVD and accompanying soundtrack. The film timings (hour:minutes:seconds) are listed on the left, with approximate corresponding timings on the soundtrack (disc #, track #, minutes:seconds) on the right.


0:00:00-0:00:21 = D1, T1, 0:00-0:21

0:00:21-0:00:28 = no music

0:00:28-0:01:52 = D1, T2, 0:00-1:24
0:01:52-0:04:23 = D1, T3, 0:00-2:31
0:04:23-0:05:42 = D2, T4, 0:00-1:18
0:05:42-0:05:47 = appears to be an artificial extension of the end of D2, T4
0:05:47-0:07:32 = D1, T5, 0:00-1:44
0:07:32-0:09:55 = D1, T6, 0:00-2:23
0:09:55-0:10:49 = D1, T7, 0:00-0:53

0:10:49-0:13:09 = no music

0:13:09-0:13:32 = D1, T8, 0:00-0:23
0:13:32-0:14:08 = D1, T8, 0:23-0:55 (this picks up right where the previous left off, but is noticeably slower, so I've analyzed it as two separate parts)
0:14:08-0:17:14 = D1, T9, 0:00-3:05
0:17:14-0:18:45 = D1, T10, 0:00-1:31
0:18:45-0:19:17 = D1, T11, 0:00-1:01

0:19:17-0:19:58 = no music

0:19:58-0:21:16 = D1, T12, 0:00-1:18
0:21:16-0:23:25 = D1, T13, 0:00-2:08
0:23:25-0:25:08 = D1, T14, 0:00-1:42
0:25:08-0:27:12 = D1, T15, 0:00-2:03
0:27:12-0:28:14 = D1, T16, 0:00-1:02

0:28:14-0:28:57 = no music

0:28:57-0:29:51 = D1, T17, 0:00-0:53

0:28:51-0:30:11 = no music

0:30:11-0:30:17 = D1, T17, 1:40-1:44
0:30:17-0:31:13 = D1, T17, 1:20-2:17
0:31:08-0:31:45 = D1, T18, 0:31-1:08

0:31:45-0:32:29 = no music

0:32:29-0:33:41 = D1, T19, 0:00-1:11
0:33:41-0:34:37 = D1, T20, 0:00-0:56

0:34:37-0:35:57 = no music

0:35:57-0:37:15 = D1, T21, 0:00-1:18
0:37:13-0:39:48 = D1, T22, 0:00-2:35
0:39:48-0:40:54 = D1, T23, 0:00-1:05

0:40:54-0:41:45 = no music

0:41:45-0:44:43 = D1, T24, 0:00-2:51

0:44:43-0:44:26 = no music

0:44:26-0:47:57 = D1, T25, 0:01-2:23
0:47:57-0:49:32 = D1, T26, 0:00-1:34

0:49:32-0:49:37 = no music

0:49:37-0:51:02 = D1, D27, 0:00-1:24
0:51:03-0:52:04 = D1, T28, 0:00-1:00
0:52:04-0:53:02 = D1, T29, 0:00-0:53
0:53:02-0:55:01 = D1, T30, 0:00-1:58
0:55:01-0:55:58 = D1, T31, 0:00-0:55
0:55:58-0:56:39 = D1, T31, 0:09-0:48
0:56:39-0:56:44 = D1, T31, 0:51-0:56
0:56:44-0:56:55 = D1, T31, 0:58-1:08
0:56:55-0:56:58 = music unknown
0:56:58-0:57:03 = D1, T31, 1:09-1:14

0:57:03-0:57:13 = no music

0:57:13-0:58:26 = D1, T32, 0:00-1:12

0:58:26-1:06:58 = no music

1:06:58-1:09:13 = D1, T33, 0:00-2:14

1:09:13-1:09:24 = no music

1:09:24-1:10:34 = D1, T34, 0:00-1:09

1:10:34-1:11:15 = no music

1:11:15-1:16:19 = D2, T1, 0:00-5:04
1:16:19-1:18:06 = D2, T2, 0:00-1:48
1:18:06-1:21:57 = D2, T3, 0:00-3:50
1:21:57-1:22:35 = unknown music
1:22:35-1:22:48 = D2, T3, 3:50-4:02

1:22:48-1:23:45 = no music

1:23:45-1:24:23 = D2, T4, 0:00-0:37
1:24:23-1:26:54 = D2, T5, 0:03-2:25

1:26:54-1:28:11 = no music

1:28:11-1:29:23 = D2, T6, 0:00-1:12
1:29:23-1:33:05 = D2, T7, 0:00-3:41
1:33:05-1:36:53 = D2, T8, 0:00-3:47
1:36:53-1:37:22 = D2, T9, 0:00-0:28
1:37:22-1:39:42 = D2, T10, 0:00-2:19
1:39:42-1:42:08 = D2, T11, 0:00-2:25
1:42:08-1:44:38 = D2, T12, 0:00-2:29
1:44:38-1:45:02 = D2, T13, 0:00-0:25
1:45:02-1:45:53 = D2, T14, 0:00-0:51

1:45:53-1:46:17 = no music

1:46:17-1:46:36 = D2, T15, 0:00-0:18

1:46:36-1:46:38 = no music

1:46:38-1:47:03 = D2, T16, 0:00-0:24
1:47:03-1:48:25 = D2, T17, 0:00-1:21

1:48:25-1:49:13 = no music

1:49:13-1:49:57 = D2, T18, 0:00-0:44
1:49:57-1:50:21 = D2, T19, 0:00-0:24
1:50:21-1:51:13 = D2, T20, 0:00-0:51
1:51:13-1:52:02 = D2, T21, 0:00-0:47
1:52:02-1:53:02 = D2, T22, 0:00-0:59
1:53:02-1:55:01 = D2, T23, 0:00-1:59
1:55:01-1:56:19 = D2, T24, 0:00-01:18

1:56:19-1:56:32 = no music

1:56:32-1:56:45 = D2, T25, 0:00-0:14
1:56:45-1:59:04 = D2, T26, 0:00-2:18
1:59:04-2:01:25 = D2, T27, 0:00-2:21

2:01:25-2:02:06 = no music

2:02:06-2:03:37 = D2, T28, 0:00-1:30

2:03:37-2:03:39 = no music

2:03:39-2:03:57 = D2, T28, 1:31-1:50
2:03:58-2:05:29 = D2, T28, 1:50-3:21
2:05:29-2:07:17 = D2, T29, 0:00-1:47
2:07:17-2:08:35 = D2, T30, 0:00-1:18
2:08:27-2:09:51 = D2, T31, 0:00-1:24
2:09:51-2:11:04 = D2, T32, 0:00-1:12
2:11:04-2:11:25 = D2, T32, 1:15-1:36
2:11:25-2:11:43 = D2, T32, 1:54-2:12
2:11:43-2:11:49 = D2, T32, 2:32-2:38
2:11:49-2:12:28 = D2, T32, 3:34-4:13
2:12:28-2:13:04 = D2, T32, 4:26-5:02
2:13:04-2:13:21 = D2, T32, 5:03-5:19
2:13:21-2:16:11 = D2, T32, 5:20-8:11

The primary musical contribution in Star Wars, Episode I: The Phantom Menace is the epic "Duel of the Fates", the ostinato of which is likely borrowed from the third movement scherzo of Antonín Dvořák's Symphony No. 9, commonly known as "The New World Symphony".

First, here's an excerpt from Star Wars. While the ostinato continues throughout the majority of the track, it is easiest to hear (despite being very quiet) from 0:15 to 0:24.

Now compare that with the Dvořák. Here, too, the ostinato is used throughout the majority of the track, but it is easiest to hear at 0:18.

While they're clearly not identical (the Dvořák is in triple meter, while the Williams is in duple, and the first half of the Dvořák ostinato has no counterpart in the Williams), the similarities are undeniable: Both are in E minor, using the notes A-G-F#-E consecutively in close but not identical rhythms (indicated in the graphic below with solid red lines). Furthermore, the first note of this pattern is comparable: F# in the Dvořák, compared to G in the Williams - a half step apart, the smallest possible interval (indicated below with the dotted red line).

Given all of that, I think it very likely that Williams' temp track for The Phantom Menace included Dvořák's Symphony No. 9.