Not really sure on the '06 model, but on '02 and '03s that i have worked on they are on top of the airbox in front of the filter, and on my '98 it is mounted on the back of the airbox in front of the rear fender, and the airbox covers the rear fender on all three, so the fender shouldn't have any thing to do with mounting the cdi, but like i said i have not seen an '06 so look and see, but i believe the airboxes are the same from '02 to '06.