Wow that didn't take me long to figure everything out. I will explain what I did to fix the issue here since tutorials online are mostly for pokemon games. Like I thought there were two pointers; the reason I did not see them sooner is because they were separated somewhat far apart from each other and their was so much code around it, so it was hard to see. A simple solution which makes me feel very stupid right now is having your hex editor find those additional values for you. (SERIOUS FACE PALM RIGHT NOW)   

Anyway I hope this will help someone in the future who's in a similar situation.

Ok so I decided to try to change around music in another rom (Sonic Advance 3) and it worked with no issues so I guess megaman and bass might have two or more song pointers? I'm not entirely sure yet. I did mess around with the rom a little more  and was able to get the music to stop playing but that's all I was able to accomplish, and it wasn't very helpful as I had to replace like 6 lines in the song table with zeros. Oh and their was on in in particular 0006A4E0 that controls all sound I believe; when I replaced that line with zeros it got rid of all sound (even sound effects) for some reason. It's surprising that 9 bytes can control all sound in a rom. Anyway I'm gonna mess around with the rom some more; any and all suggestions are appreciated. If I find a solution I will post it here just in case anyone else has a similar issue with their rom.

I am using sappy to make a music hack of (Megaman And Bass GBA) and for awhile when I was importing tracks I would overwrite the non custom songs header with the custom songs header after running into some issues I don't want to do that, but when I move the songs header somewhere else in the rom the song won't play in game, it will only play in sappy. Any kind of help would be appreciated.