Interesting on the quality of the BD5. I have built my BD5 any didn't have any of the same issues. The anodizing all matches and seems high quality. My deck lines up perfectly. I also like the servo mount. I don't have pulley clearance issues for the center pulleys.
I was wondering if you had the front and rear (left and right) bulkheads in correctly. I almost put mine in wrong. I believe that may cause an alignment issue.