Non-recoverable Exception 3 when building with GCR

I'm working on my own custom mods using this codebase as a starting point and I am unable to get a working ISO built. I have done the exact same steps with both my modified branch as well as the original master and gotten the exact same results each time, which is why I'm opening the issue here.

Steps Taken:

1. Extract vanilla Melee 1.02 ISO with GCR
2. In the resulting root folder, remove files "MvHowto.mth" and "MvOmake15.mth" to make room for additional files
3. Replace aforementioned files with renamed copies of "MvGanonEnd.mth"
4. Run the .bat file in the Build TM Codeset folder as per README instructions to generate codes.gct
5. Drag the vanilla Start.dol onto the .bat file in the Build TM Start.dol folder as per README instructions to patch Start.dol
6. Replace root/&&systemdata/Start.dol with new Start.dol
7. Move all other additional files and folders to root folder
8. Open GCR and select "Do not use game.toc" from options menu
9. Open modified root folder
10. Save to ISO and Rebuild
11. Copy new ISO to USB:\games\GALE01\game.iso
12. Attempt to load ISO in Nintendont on modified Wii

When Nintendont lists the games on the USB drive, it recognizes a valid Melee 1.02 ISO, and it does indeed execute however all I get is a black screen. Thankfully, Nintendont has debug logging so I am able to see that when the game runs, there is a Non-recoverable Exception 3 with all kinds of memory addresses and the message, "Attempted to fetch instruction from invalid address 0x0 (read from SRR0)."

I have also tested with Dolphin; it does not work there either.

Here is the complete ndebug file: https://pastebin.com/uAxHnY7C