These patches won't run correctly when re-injected on the gamecube disc.
It ended up working on the collectors edition, after replacing Majora's Mask rom, and making a simple hex edit to the patched Master Quest rom.
replace zelda2e.n64 with patched urazle_f.n64
open hxd or some other hex editor and replace:
THE LEGEND OF ZELDA .......CZLE
with
ZELDA MAJORA'S MASK .......NZSE
Because Majora's Mask uses the 8mb expansion, it will now load.
Edit: I took it a step further and replaced the urazle.tpl and urazle_f.n64 with the modded zelda2e.n64 and default zelda2e.tpl and it worked.
Edit2: Though putting it back into the disc version of Master Quest does not