After an entire fucking week of attempting to make a working Majora's Mask Redux patched WAD, today I finally made one that doesn't fucking crash in Dolphin.
Went from:
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To:
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Was a fucking painful learning experience, because I thought that maybe the ID was causing troubles, so I attempted multiple different ones. Once I realized that it wasn't the problem, I tried different WAD files from multiple sites and even WAD files I had stored in my Google Drive, as I thought that maybe the WAD files were corrupted or something.
That didn't seemed to matter neither.
Each time my patched WADs crashed it deleted my Save File entirely, so that meant that I had to restart the fucking game from scratch just to test every little fucking change I made to the options.
I even tried to skip the Intro (start the game at Clock Town) and even tried patches skipping the entire first cycle, but that also wasn't a problem. I thought this as a variable as maybe the game expected to check flags or something in order to prevent the crashes. But nope.
Then I tried different builds with the same options as I thought that maybe something was getting corrupt during the patching process and perhaps with different builds, the "whatever is getting corrupted" wouldn't... but nope.
Then I tried the bare minimum of improvements, and that seemed to have fixed the issue. I don't know what option is fucking corrupting the game in such fashion that crashes the game at cutting bushes. I certainly can't put my finger on what might be as I tried literally hundreds of different combinations and never could get a "a-ha" moment. But whatever... it fucking works now!