I have this MPU6050, and like most of the other MPU6050s, it is set up for SCL to be attached to A4 and SDA to be attached to A5. I have this shield on my Arduino Uno, which is configured for Sainsmart's (the company who made the shield) MPU6050, so the special MPU6050 pins are set up V, G, A5, A4, and my current setup needs V, G, A4, A5. I am using the built-in Wire library, I2CDev library, and the MPU6050 library. So I am wondering whether there is something in these libraries that define which pins it looks for my MPU6050 on, and if so how do I change it.
The pin definition is in hardware. There is nothing you can do to change it. However you could try to reprogram it to use a software i2c library instead of the hardware wire library.
Why not build a small board that converts the pins from V, G, A5, A4 to V, G, A4, A5? Or modify the PCB e.g. cut and rewire the signals in the order you want. It is only two pins!