In the manual there is a long and involved process for alignment and I've never done it, though I have string lined my bike. I fitted a ridestr8 and found that made an improvement for pushing hard.

If you like you can download a PDF under my DIY (Do It Yourself) section found here.  That should help you out  LINKY:

Hey Fast, there are good articles on this site including how to align the rear wheel. I guess the only thing about it is that it does not go into engine alignment but the principles are there on checking the overall lines. Thanks.

HB, I have just put my 08RKC on a bike lift and made it level, measured it on the underside of the cross member (where the lift fits in). I then put a level on the back disc and on a chord running adjacent the disc mounting bolts and found the disc was out of plumb by 5mm over the length of the disc or with the protractor 1.5 degrees. The front wheel was plumb. Its hard to check but I put a level along the top of the handlebar clamp shroud and turned the bars till it showed level and then checked the plumb of the wheel. So what you have been saying is pretty spot on. How much out of plumb was your back disc?