As I read your post, before I even got to this point, this is what I was thinking. When you did the headset rebuild...did you remove the top and bottom races/cups from the headtube? If so are you SURE that you got them back in correctly? I.e. there is a top and bottom race. I once had the same exact issue after a rebuild with the bike pulling to the left after the job when it hadn't pulled prior to the job. Eventually I took the headset all apart again and only then noticed that there is a slight difference in the top and bottom races. I swapped them and reassembled, and then it ran perfectly straight.

Dan