When I put in flattops, cam, header, port work. etc on my L6 years ago, the only thing that would help was to LOOSEN the spring on the AFM...
* caution * mark where it exists now and very carefully loosen the nuts that hold it (because it can all come untensioned) ... then let the tension off of the spring. I would do this in incremental steps to get it to run as well as you like it to.