Right then, so I determined using Melee's md5 check method that I have version 1.0 of Metroid Prime, yet neither the direct conversion of the AR master codes, nor Link's custom master 1, (master 2 is just a direct conversion of "Must Be On") will allow me to get any farther than the area name screen without the game crashing.
The codes I'm trying to run are infinite health:
04049EA8 48000104
And a conversion of Have Phazon Cannon Everywhere:
2C458244 FF000080
287A55A8 FF0000C5
00458245 0000007C
E2000001 80008000
28457D32 FF000000
287A55A8 FF00003B
00458245 000000FE
E2000001 80008000
Now, I'm nothing if I'm not thorough. As I've already mentioned, I confirmed the version number by cross referencing the iso's md5 checksum with listings on redump.org, and I have double checked my settings in GeckoOSMod. (Yes I still use it, because frankly I still find it much more stable for Gamecube hacking than Neogamma which I can't seem to run at all) I even went out of my way to test and succeed in getting codes working in Super Mario Sunshine, a game I had previously worked with near flawlessly. I was not disappointed this time around. I also tried a direct conversion of the AR master code to no avail, and thus I come here, completely out of ideas, sans one Phazon cannon.
ALTERNATIVELY, if anybody would like to take the time to remake said Phazon Cannon code for Metroid Prime Trilogy, that would work for me just as well, if not better, since I sort of prefer the controls in that version anyways. That being said, if anybody can be of assistance here, it would be greatly appreciated.