I believe the teensy will help and to clarify, I am planning to take the sp apart into two parts, the screen which will be sticking out of custom made case housing all the electronics for the midi controller, and the gameboys buttons which will be mounted and sticking out of the case just like how they would a normal gameboy. Here is a very bad mockup of my design: http://www.deviantart.com/art/Design-451168437

Can you draw a mockup of what you are trying to do? Will the gameboy hardware be used at all, or are you just using the case? You might want to check out:
http://www.pjrc.com/teensy/
http://www.pjrc.com/teensy/td_midi.html

Can someone help me with a Idea I've been having. I want to build a midi controller ( the drum pad like one with the squares) that I can plug into a gameboy advance sp ( I would use a dmg but I want to build the gameboy into the controller and have the screen come out of the controller box at an angle and then have the normal buttons laid out flat on top of the box) then have the grid laid out so eat vertical row is a octave ( c, c#, d, f, e, etc.) and each horizontal column is a different note ( 2, 3, 4, etc.). I was wondering if someone could help me with connecting the midi controller and making sure everything lines up right. Thank you to anyone who can help me.