It's not always the 4th. Every non-null 32-bits is a track in the exported midi from N64 Midi tool.So you find right track, and null out corresponding raw bin track offset.
If I recall correctly VGMTrans can find midi sequences in some roms (Chameleon Twist 2, Super Smash Bros, Mischief Makers, to name a few) and if you expand the selection it can identify different instruments.
Edit: It's half an idea. I really should learn to piece together what I'm saying before I post it.
Since I begged for it last time, I'll say the one thing I know about this (although I'm not sure if you're beyond that point); apparently, in order to do what you're asking, as far as muting certain channels, you have to figure out which call string it has in the hex code, and zero it out in that particular USF file.
I got about as far as you did, but Josh W managed to do it properly for me, which is why we have versions of Tooty's Theme without the lava bubbling and furnace blasting, and inside the Rusty Bucket without the gears squeaking.