PaulS:
You can apply external power via the jack and power via the USB at the same time. The Arduino has circuitry to determine which one to actually use.If you bypass the jack, and supply 5V directly to Vin, then you've bypassed the safeguards, too. But, you wouldn't be putting 9V into Vin.
So, it isn't clear how you are powering the Arduino.
The Micro's web page states "External (non-USB) power can come either from a DC power supply or battery. Leads from a battery or DC power supply can be connected to the Gnd and Vin pins.
The board can operate on an external supply of 6 to 20 volts. If supplied with less than 7V, however, the 5V pin may supply less than five volts and the board may be unstable. If using more than 12V, the voltage regulator may overheat and damage the board. The recommended range is 7 to 12 volts. "
I used an ON Semi MC78L00A 9V voltage regulator to get 9V out of the 12-14V from the motorcycle. Ground from the regulator is tied to the Micro's ground and the output of the regulator is tied into VIN. So have I misread this?