Given that the multitracks were copied en masse, this is unsurprising. As for 10452 and the AFM contracts, my understanding is that the song titles were listed in order if recording. Corrections and additions etc., etc....
Other than the first day, the order of tunes is a little difficult since they didn't stay on one tune until they got a master, they'd do a few songs, do a few more, come back to the first batch, etc. But I'd say "Barbara Ann" was the last tune they did on September 23, for instance.
Here is the order I came up with; I can't guarantee it's 100% in order but I think it should be in the ballpark. The "master" takes don't appear to be included within the session takes, unless I missed them. I'll admit to getting a bit of ear fatigue after the millionth version of "Hully Gully", so no guarantees here!
First number is the disc number, second is the track number. The numbers in the track names are from the SOT track names and the order they appear on those discs, so don't necessarily correspond to the correct order overall (which is why "Bob Dylan Parody #2" appears before "Bob Dylan Parody #1", for example.)
1 01 Tuning Up [8/23/65] 1:47
1 02 I Should Have Known Better #1 [8/23/65] 2:31
1 03 Ruby Baby #1 [8/23/65] 2:15
1 04 Satisfaction #1 [8/23/65] 2:16
1 05 Hully Gully #1 [8/23/65] 2:03
1 06 Blowin' In The Wind [8/23/65] 3:12
1 07 Talk Between Sessions #1 [Sunrays Chat] [8/23/65] 4:45
1 26 Talk Between Sessions #6 [9/8/65] 1:38
1 27 Hully Gully #2 [9/8/65] 3:28
2 01 Satisfaction #2 [9/8/65] 2:12
2 02 Ruby Baby #2 [9/8/65] 2:36
2 03 Hully Gully #3 [9/8/65] 3:17
2 04 Satisfaction #3 [9/8/65] 2:07
2 05 Talk Between Sessions #7 [9/8/65] 1:19
2 06 Ruby Baby #3 [9/8/65] 3:28
2 07 Talk Between Sessions #8 [9/8/65] 1:10
2 08 Ruby Baby #4 [9/8/65] 3:17
2 09 I Should Have Known Better [9/8/65] 2:46
2 10 Tell Me Why [9/8/65] 1:23
2 11 You've Got To Hide Your Love Away #2 [9/8/65] 2:58
2 12 Talk Between Sessions #9 [9/8/65] 1:00
2 13 Little Deuce Coupe #2 [9/8/65] 1:49
2 14 California Girls [9/8/65] 2:26
3 04 Talk Between Sessions #16 [9/8/65] 1:47
3 05 Hully Gully #4 [9/8/65] 2:21
3 06 Ruby Baby #5 [9/8/65] 2:11
3 07 Talk Between Sessions #17 [9/8/65] 2:33
3 08 Hully Gully #5 [9/8/65] 3:10
3 09 Ruby Baby #6 [9/8/65] 2:23
3 10 Talk Between Sessions #18 [9/8/65] 2:50
3 11 Hully Gully #6 [9/8/65] 3:32
3 12 Talk Between Sessions #19 [9/8/65] 2:27
3 13 Hully Gully #7 [9/8/65] 1:58
3 14 Hully Gully #8 [9/8/65] 2:25
3 15 Talk Between Sessions #20 [9/8/65] 1:30
3 16 Hully Gully #9 [9/8/65] 3:31
1 18 Bob Dylan Parody #2 (She Belongs To Me-I Got You Babe) [9/8/65] 2:50
1 19 Talk Between Sessions #4 [9/8/65] 1:27
1 20 Riot In The Cell Block No.9 #2 [9/8/65] 1:29
1 21 Talk Between Sessions #5 [9/8/65] 1:43
1 22 Diary [9/8/65] 2:19
2 15 Talk Between Sessions #10 [9/14/65] 2:06
2 16 Tell Me Why #2 [9/14/65] 1:39
2 17 I Should Have Known Better #3 [9/14/65] 1:54
2 18 Talk Between Sessions #11 [9/14/65] 1:08
2 19 Mountain Of Love #3 [9/14/65] (Take 1 on official) 2:56
2 20 Devoted To You #1 [9/14/65] 1:30
2 21 Talk Between Sessions #12 [9/14/65] 1:41
2 22 Devoted To You #2 [9/14/65] 1:30
2 23 Devoted To You #3 [9/14/65] 1:31
2 28 Talk Between Sessions #15 [9/14/65] 1:07
2 29 Devoted To You #4 [9/14/65] 1:45
2 30 Devoted To You #5 [9/14/65] 3:01
2 31 You've Got To Hide Your Love Away #3 [9/14/65] 4:26
1 23 Unknown Piano Piece (Little Honda) [9/14/65] 1:13
1 24 Alley Oop #1 [9/14/65] 4:56
1 25 Alley Oop #2 [9/14/65] 2:48
3 01 Alley Oop #3/Ticket to Ride/Alley Oop #4 [9/14/65] (#4 is Take 1 on official release) 6:54
3 02 There's No Other (Like My Baby) [9/14/65] 5:02
3 03 Devoted To You #6 [9/14/65] 4:21
1 08 You've Got to Hide Your Love Away #1 [9/15/65] 3:19
1 09 Talk Between Sessions #2 - I Get Around (parody) [9/15/1965] 3:53
1 10 Little Deuce Coupe #1 [9/15/65] 2:37
1 11 Mountain Of Love #1 [9/15/65]* 5:26
1 12 Mountain Of Love #2 [9/15/65] (Take 2 on official) 2:31
1 13 Talk Between Sessions #3 [9/15/65] 1:03
1 14 Ticket To Ride [9/15/65] 1:33
1 15 Riot In The Cell Block No.9 #1 [9/15/65] 4:57
1 16 Bob Dylan Parody #1 (Laugh At Me) [9/15/65] 2:35
1 17 One Kiss Led To Another [9/15/65] 3:44
2 24 Talk Between Sessions #13 [9/15/65] 2:11
2 25 Mountain Of Love #4 [9/15/65] 2:21
2 26 Talk Between Sessions #14 [9/15/65] 3:51
2 27 Mountain Of Love #5 [9/15/65] 2:49
3 17 You've Got To Hide Your Love Away #4 [9/26/65] 5:20
3 18 The Times They're A-Changin' #1 [9/26/65] 3:49
3 19 Heart And Soul [9/26/65] 0:50
3 20 Talk Between Sessions #21 [9/26/65] 1:32
3 21 The Times They're A-Changin' #2 [9/26/65] 1:56
3 22 Heart And Soul-Long Tall Sally [9/26/65] 1:21
3 23 Smokey Joe's Cafe #1 [9/26/65] 2:26
3 24 Smokey Joe's Cafe #2 [9/26/65] 1:27
3 25 Barbara Ann (Takes 1-2) [9/26/65] 5:37
If you see anything glaringly wrong, please let me know! 9/8 is where I'm particularly unsure of the correct order of tracks.