Hey Bajabomber87,
I just acquired my 1st Buell - it's an '06 XB12R - this bike does the exact thing you described in your first post above. I didn't see your bike's year but I'm wondering if you still have the repair invoice and if you have any advice as to what exactly I need to replace in the transmission. I probably will post my own troubleshoot thread on this but wanted to ask you since you've already went thru this repair.
Thanks for you help.
Originally harley replaced a shift fork and a dog gear. This lasted about 3-4k miles before I started getting the same problem. After warranty was up, I rebuilt the tranny myself and the shift cam ended up being worn out causing the forks to wear prematurely.