Micron Exhaust

I have recently acquired a 2009 xb12r with a micron exhaust installed with no ecm modifications completed, so the check engine light is on. What do i need to do to take care of this? Can you flash the stock ECM to correct or do i need to get an a/m powers commander type ECM?

How do you know the stock ECM isn't modified?

Adding a aftermarket exhaust won't cause a check engine light. There is an issue you need to find before modifying anything.
It is very possible the light is on because the aftermarket exhaust no longer has the solonoid on it. Pretty common.
You can jumper the pins to get the trouble code, but with all the things you want to do I would heavily suggest you get a dongle and ECMDroid.

You can put a program on your stock ECM for free by using ECMDroid that connects using a Bluetooth wireless dongle. You can find manuals and maps at Buellmods.com or Buelltooth.com

You can also buy an ECM from IDS.com that will have the program you need on it already. You will still need to diagnose the light.

There are nice people on this board that can do that job for you as well. I believe AZMidget still does this?

I personally think piggy back "power commanders" are pointless for this make of bike when the ECM programming is so easy and cheap:)