I would check carefully the rear wheel to frame alignment, and don't trust the frame marks to be correct. Use a caliper and check bolt lengths in there, and see what you get. I take it the front end is tight, no looseness.
I am going to be building an engine using the CycleX 849 coated pistons. What cam did you use? I am running a Kenny Harmon D grind on stock pistons, and it is totally unacceptable as a street cam. Will not idle. 5000 RPM to over 10K it's very happy. I am thinking with the 849 kit though, compression will be high enough at idle to use that cam without a problem, and no knocking, because the cam has such high overlap.