I had a cam cut / welded, and shipped directly to a shop in California for a Shell #1 cam grind.
Got it back and there was too much run out on it.
So then I got a properly rephased cam from the guy who pioneered cutting / using positioning pins / bolting it back together. Had that one done with a nice cam profile and it worked a treat. Mrriggs was the guy for this back in 2011.
http://www.xs650.com/threads/rephasing-the-cam-shaft.7403/
How are you putting the cam back together? Did you drill the positioning holes before cutting?