I hope everything I write here is correct. I'm not 100% sure.
The MPU-6050 code by Jeff Rowberg used INT0. This is fixed in his code I think.
That is digital pin 2 (D2).
This is the same for an Arduino Uno and an Arduino Mega 2560.http://arduino.cc/en/Main/arduinoBoardMega2560
The I2C is on other pins, but you have that part working.
The MP3 shield used also D2 for MP3-DREQ.
I think the others pins are no problem, but only D2.
Since D3 and D4 are in use with the MP3 shield, you have to use pin 18 (interrupt 5), 19 (interrupt 4), 20 (interrupt 3), or 21 (interrupt 2) of the Arduino Mega 2560.
So the software for one of the shields much be changed for the new pin.
For the mp3 sketch, I see this:
#define VS_DREQ 2
The VS_DREQ could be set to a different pin. But you also must change the SoftwareSerial call, even the RX for pin 2 is not used.
In your sketch I see that TIMER1 is used. I don't know if that is already in use for another library.
Perhaps you should place the code in three different files (use the drop-down icon on the right of the tab bar in the Arduino IDE).