You can ask about any bike you like mate... bike is a bike.
Now, as for your problem... I don't know if those two r/rs are interchangeable but if the stator or the 06R6 is designed to put out a higher voltage then it may have damaged the r/r, or it could just have come broken...
Can you post up a pic of the connector?
Thanks for the response!
A little more background on the situation. His bike started having "draining the battery" issues and after checking out things it came to be the stator. So we changed it out for a new 2004 R6 stator.
A few weeks later unfortunately, he was in a small accident where he rear ended a car (Couldn't stop quick enough) and long story short, somehow the r/r blew shortly after the accident. (he had the typical signs of a bad rectifier, burnt wires and melted plug...I guess his year bike is known to do that)
Anyways, he found a guy/shop (not sure exactly) that supposedly does a lot of work on r6's and he says to do a swap for a 2006 year r/r because it solves the problem. Told him to order the connector (on ebay i think they have them or some website the guy showed him) and sold him a "new" rectifier.
Anyways, the new connector came with wires already attached so it was just a matter of soldering black to black and red to red, plus the three white wires. (these are the wires I soldered to the same locations as the previous r/r plug)
here are two pics. (hopefully they help). The red wire looks grey because of the heat shrink tubing.