I installed a set of kw clubsports on my E90 M3 tonight. I had no problem aligning the bolt for the rear lower suspension arm on either side, so I figured I would post exactly what I did and hopefully it helps others since this seems to have tormented more than a few people...
On the first side when I removed the bolt I noticed that wheel carrier moved in towards the center of the car slightly. After I swapped out the spring and shock I used a jack under the rear lower suspension arm to start raising it back up. When I got the arm up to the point where the wheel carrier was close to where it should be I looked through the bolt hole and sure enough the alignment was off by at least 2-3 millimeters.
Now this lower arm is adjustable in/out to adjust rear toe, so I figure if I losened the inner bolt it may help with the alignment. First I marked the current position of the adjuster lobe so I could easily put it back where it was. I then loosened it and adjusted the lobe so that it pulled the arm in towards the diff. I the checked the alignment of the bolt hole again and they were now very close. I then jacked the arm up a bit more and then with one hand moved the wheel carrier up a bit further. The alignment now looked near perfect and I was able to easily slide in the bolt.
I finished assembly and then move on to the other side. Same thing happened there again when I removed the bolt. I followed the same procedure again of loosening the toe adjustment, pulled the arm in and again I was able to just slide in the bolt. Super easy.
If I didn't loosen the toe and pull in the arm it would have been much much harder to get them aligned.
Make sure to return the toe adjustment to where it was previously before you tighten things up. Really a full alignment should be done after a spring install anyway, but at least you will be close to where previously. Also make sure the suspension is compressed when tightening these bolts so the bushings aren't binding.