Hi, when you talk about something please give a link to it.
Joop Brokking YABR: Brokking.net - Your Arduino Balancing Robot (YABR) - Home.
Sparkfun SAMD21: SparkFun SAMD21 Dev Breakout - DEV-13672 - SparkFun Electronics
When something is wrong, fall back to something simple basic that you can make work. For example a minimal sketch that shows the problem. Now you have created a sketch that has already too many issues.
First of all, you could have bought a real Arduino board for better support. For example the Arduino Zero or the MKR Zero, or even a Arduino M0 clone like the Elecrow M0-SD.
Have you installed extra Sparkfun boards for the Sparkfun SAMD21 ? Did it come with its own Wire library ?
Stay away from the TWR or SERCOM. The Wire.setClock() is the function to set the clock.
Since there are problems, you should use the default 100 kHz. Increasing the clock is for when everything works perfect.
Run the I2C Scanner and find the address of the sensor. Use that with the shortest example possible: Arduino Playground - MPU-6050. That example uses "int16_t" to create the x,y,z value. That is what is needed. You try to put them directly into parameters for the SerialUSB.print() function, that is asking for trouble.
Don't do this after a Wire.requestFrom(): while(Wire.available() < 2);Did someone tell you to do that ? or did you found a (wrong) example ? You can remove all of them, there are about 4 of those in the sketch.
You test if the I2C address is 0x68 or 0x69, but after that you assume it is 0x68.
It is not a well structured sketch. You could put more code in functions, and design a better program flow.
How is your I2C bus ? I hope just a few short wires and not a cable.
Since the SAMD21 is a 3.3V processor, you don't need level shifters anymore for the I2C or SPI bus. The MPU-6050 is noisy, you could upgrade to the MPU-9250. The MPU-9250 can be used with I2C and SPI.