There are tabs in the casting that will locate the pickups to the stock assembled positions. Technically, the pickups are interchangable physically and electrically, however, there is a right and wrong place for each when matching the color code of the schematics.
The pickup for the front cylinder is mounted in the 8:00 position, and has wire colors of Black/yellow and solid black.
The pickup for the rear cylinder is mounted in the 10:00 position, and has wire colors of Black/White and Black/Red.
Mount them in the correct positions, and match the wire colors to the wire colors of the 4 pin connector that leads to the IC ignitor.
That being said, you may want to consider the pickup coil mod described on this site. Basically, the mod moves the pickups closer to the flywheel; .018"~.020" from the flywheel. I did it to my bike in conjunction with new iridium plugs, and I know that I have no more issue with hot starts. Research the mod. It is easy. And decide if you might want to do it, if you have hot start issues, since you are working in there anyway.
Last edited by ZCraggRatt; 03-16-2012 at 12:37 PM.