Remember:

*** bd1978-07-12d1t15-d2t01.merge.shn replaces BOTH bd1978-07-12d1t15.shn AND bd1978-07-12d2t01.shn ****

In other words, you have two choices here.  You can go either with the unmerged version or the merged version.  Below is what the two version should look like:
-----------------------------------------------------------

unmerged version

disc 1

13. Going, Going, Gone
14. Rainy Day Women # 12 & 35  - alt. "patch" source (bd1978-07-12d1t14.shn)
15. True Love Tends To Forget - alt. "patch" source (bd1978-07-12d1t15.shn)

disc 2
1. True Love Tends To Forget (bd1978-07-12d2t01.shn)
2. Gates Of Eden (bd1978-07-12d2t02.shn)
3. The Man In Me
---------------------------------------------------------

merged version

disk 1 

13. Going, Going, Gone
14. Rainy Day Women # 12 & 35  - alt. "patch" source (bd1978-07-12d1t14.shn)
15. True Love Tends To Forget (bd1978-07-12d1t15-d2t01.merge.shn)

disc 2

2. Gates Of Eden  (bd1978-07-12d2t02.shn)
3. The Man In Me