A few notes:  I gave all the OST material a 2.5db-3db boost to match it's volume to the OST.  I had to listen carefully to match the volumes of the game material to the OST/UE material.  Also, the game material was generally about 10cents faster than the UE/OST material.  Much of the UE material had to be checked for looped segments and edited accordingly.
 

Track 01	Fox Fanfare	UE CD Track 1
Track 02	Star Wars Main Title	UE CD Track 2
	Boarding the Federation Battleship	UE CD Track 3
	Death Warrant for Qui-Gon Jinn and Obi-Wan	UE CD Track 4
	Fighting the Destroyer Droids	JPB Track 5a
		UE CD Track 5 (0:28-end)
	Queen Amidala Warns the Federation	UE CD Track 6
	The Droid Invasion	UE CD Track 7 (0:00-0:05)
		OST Track 14 (1:10-1:36)
		UE CD Track 7 (0:34-0:43)
		OST CD Track 14 (1:36-1:44)
		TPM sqdanger1.imc (use the end of UE Track 07 for last chord ring out)
Track 03	Jar Jar Binks and the Swim To Otoh Gunga	OST Track 4 (0:00-2:02)
	(segue material)	UE track 8 (0:50-end)
	Inside the Bubble City/Attack of the Giant Fish	OST Track 10
Track 04	Darth Sidious	UE Track 11
Track 05	The Giant Squid (opening)	UE Track 12 (first two beats)
	The Giant Squid and Attack on Theed	OST Track 14 (2:09- 3:15)
	The Attack on Theed (closing)	UE Track 12 (last chord, goes right into next track)
	Qui-Gon and Obi-Wan Rescue the Queen	UE Track 13 (0:00-1:47)
		TPM CDROM sqtheedattack.imc
	Fighting the Guards	UE Track 14 (0:00-1:13)
		OST Track 12 (2:40-end)
	Escape from Naboo	UE Track 15
	Enter Darth Maul	UE Track 16
Track 06	The Arrival at Tatooine	OST Track 7 (0:00-0:24)
		UE Track 17 (0:30-end)
	Street Band of Mos Espa (source music)	UE Track 18
	Padme Meets Anakin	UE Track 19 (0:00-1:00)
		EP 1 INSIDER'S GUIDE "Hit The Nose!"
	Desert Winds (Source music)	UE Track 20
	Jar Jar's Run In With Sebulba	UE Track 21
	Anakin's Home and the Introduction of C-3PO	UE Track 22
Track 07	Darth Sidious and Maul	UE Track 23
Track 08	Talk of Podracing	UE Track 24
Track 09	Watto's Deal/Shmi and Qui-Gon Talk	UE Track 25
Track 10	Anakin, Podracer mechanic	UE Track 26
Track 11	The Racer Roars to Life/Anakin's Midichlorian Count	UE Track 27
Track 12	Darth Maul and The Sith Spacecraft	UE Track 28
Track 13	Mos Espa Arena Band (Source Music)	UE Track 29
Track 14	Watto's Roll of the Die	UE Track 30 (0:00-1:45)
	(The Probe Droid)	OST Track  11 (1:23-1:37)
	The Flag Parade	OST Track 7 (1:52-end)
Track 15	Sebulba's Dirty Hand/Qui-Gon's Pep Talk	OST Track 9 (0:00-1:36)
	Sebulba's Dirty Hand/Qui-Gon's Pep Talk (clean ending)	UE Track 32 (1:26-end) (last chord)
Track 16	Anakin Defeats Sebulba (opening)	UE Track 33 (first chord)
	Anakin Defeats Sebulba	OST Track 09 (1:36 - end)
	Hail to The WInner, Anakin Skywalker	UE Track 34
Track 17	The Street Singer (source music)	UE Track 35
DISC TWO
Track 01	Anakin is Free	UE Track 01
Track 02	Qui-Gon and Darth Maul Meet	UE Track 02
Track 03	Anakin and Group To Coruscant	UE Track 03
Track 04	The Queen and Palpatine	UE Track 04
Track 05	High Council Meeting	UE Track 05
Track 06	The Senate	UE Track 06
Track 07	Anakin's Test	UE Track 07
Track 08	Qui-Gon's Mission/Obi-Wan's Warning	UE Track 08
Track 09	Nute and Rune Confer with Darth Sidious	UE Track 09
Track 10	The Queen and Group Land on Naboo	UE Track 10
Track 11	Jar Jar Leads Group to The Gungans	UE Track 11
Track 12	War Plans	UE Track 12
Track 13	Darth Sidious Recieves News of the Gungan Army	UE Track 13
	The Gungan March (alt version)	JPB Track 6j
	The Gungan March (final version)	OST Track 14 (0:00-0:30)
	The Gungan March (clean ending)	TPM sqstalk1.imc
	Activating the Battle Droids	JPB Track 6j (opening chord)
		OST Track 14 (0:32-1:06)
		JPB Track 6j (segue between OST 14 and UE 15)
	The Queen and her Group Sneak Back to the Palace	UE Track 15
	The Battle Begins	TPM CDROMsqfight5.imc
	(download ejbon.zip for examples of how this sounds)	OST Track 14 (1:44-1:58)
		TPM CDROM sqfight5.imc
		OST Track 14 (1:58-2:08)
		TPM CDROM sqfight5end.imc
Track 14	The Hangar Battle	OST Track 12 (0:00-0:36)
	(download ejbon.zip for examples of how this sounds)	UE Track 17 (0:54-1:00)
		JPB Track 4a
		OST Track 12 (0:36-1:11)
		JPB Track 4a
		UE Track 16
		JPB Track 4a
		JPB Track 5b
		UE track 19 (0:00-0:08)
		OST Track 12 (1:18-1:44)
		TPM CDROM sqassaultintro.imc
		OST Track 12(1:44-2:40
		TPM CDROM sqsuccess1.imc (for clean ending)
Track 15	The Droid Battle	OST Track 5 (0:00-
	Ascension Guns	TPM CDROM sqgripping1.imc
	Choral Edit Piece	TPM CDROM sqmaulduelstart.imc
	The Great Dual (sic)	TPM CDROM sqfightmaul2.imc
	The Invisible Wall	UE Track 25
	The Gungan Battle	RACER Podloop1
	(download ejbon.zip for examples of how this sounds)	UE DISC 1 Track 33 (1:44-end)
		TPMsqfightmaul2end.imc
Track 16	Anakin's Crash Landing	UE Track 26 (1:36-end)
	Qui-Gon Gets Mauled	UE Track 27 (0:00-0:48)
	(download ejbon.zip for examples of how this sounds)	OST Track 15
Track 17	Anakin Destroys The Federation Ship (download ejbon.zip for examples of how this sounds)	UE Track 28 (0:00-1:31) (superimpose TPM CDROM sqreactor.imc over the opening phrases)
Track 18	The Deaths of Darth Maul and Qui-Gon Jinn	UE Track 28 (1:47-end)
Track 19	The Queen Confronts Nute and Rune/ The Funeral	OST Track 16
Track 20	The Parade	UE Track 31
	End Credits	UE Track 32

If you've made it this far, you might see there are a few files that are still left over.
I took these files and made a bonus track out of them.  The files are:
    Track 14    3:20-3:45 (Spooky synth music)
    TPM CDROM sqscary2.imc (string swell)
    UE Disc 2 Track 20 (0:03-0:23)
    RACER "ConflictLoop" (orchestra-only version of "Duel of the Fates")
    TPM CDROM sqplayerdeath.imc (an unused cadence)
    RACER "ConflictLoop2" (unused mix of the concert version of "Duel of the Fates")

It's not the most gracefully edited track in the history of recorded music, but it works for me.  I certainly find it more listenable than that ridiculous bonus track on the UE, "Duel of the Fates (movie dialogue and sound effects version)".  Who's idea what THAT?!