Can anyone help diagnose?

[IronChip]

Thanks everyone for the suggestions. After 3 weeks of research, testing, trial and error, it turns there were two issues. Chicknstripn was correct, the bike was overheating. I didn't know how to set the static timing with the '08 flywheel after the rebuild, because there is no timing mark. I basically listened for a smooth idle and rev. A week ago, i was working at night, after verifying for the 10th time that the regulator charges when the bike is cool, and let the bike warm to operating temperature. The exhausts were glowing red. It all came clear that the timing was retarded.

[Chicknstripn]

Check out the last post on this old thread. Might help you get you timing more in the ballpark.
http://www.buellxb.com/forum/showthr...07-XB12R/page2
You might want to contact the company you got your build parts from. I know NRHS has a lot of helpful information on their site. Dan was real helpful during my build.
Good luck