Very familiar with the internals of the damn cheap clutches they put in these bikes. I had more issues with mine when BigDog Tampa was still around. I've replaced the clutch pack, pressure plate, etc (all in the past), so I'm familiar with the inner workings of the primary. I've never taken the transmission apart, however BDTampa did a couple times when they were trying to figure out all the clutch slippage (before it was determined that the pressure plates needed to be anodized).
Why would the "jumping" be in third gear only? That would indicate something in the transmission, not the clutch hub nut, right?
all joking aside.
Start simple, adjust your clutch, see if that helps.
Then drain your primary, pull the cover and inspect your clutch plates , carrier, etc..carefully.....and go from there before going into the tranny....
check all other exterior adjustments/equipment before ruling them out and going towards the trans....meaning....clutch, shift linkage etc.....
if it gets to the trans, pull your top cover and check the shifter prawl adjustment and the shifter forks and look at everything in the shifter cam.
Doing it only in third gear is very odd indeed!!!
Baker trans are damn good trannys......if it's not the clutch pack, adjustments , other shit etc...could be the shifter fork or clutch DOG not sliding into 3rd gear properly.
If it's dragging or grabbing, could be a groove in your clutch basket causing plates to bind or plate lugs...but again, only third gear is odd...
Thinking about your trans comment, that would indicate that the 'dogs' on the third gear in your trans could be rounded.....
START WITH THE SIMPLE SHIT FIRST AND DON'T OVERTHINK LIKE I DO!!!