I presume you drew the patten on to see where the high and low spots were? Or were you having a Rolf Harris moment?
I'm surprised the non extreme was also quite uneven - looking at the base of mine it looks like the extra heatpipes are the cause of the warped base.
Edit: I've also considered lapping the IHS on the CPU but thought I'd wait until I've had it a week or two first... Was the IHS quite uneven too? I've read various posts saying that they are now a lot flatter than they used to be. I guess the killer question is how much benefit you've seen after lapping both?