I did my wheel alignment with the plane in level flight attitude. My reasoning was: the most critical time when squirrliness and ground looping is during fairly hi speed tail-up takeoff roll and landing rollout after wheel landing which tend to be at higher speed than 3-pointers. My gear was dead nuts at neutral with no shims in level attitude and I just left it that way. I do most of my landings 3-point and it seems to behave well in that attitude also. This is just my thinking, but I also see the logic in John's post.