It seems to be a problem if don't break it in with variable throttling for 45 minutes like you should.
Instead you would have to tune the bike before you could properly apply various throttle. Only 2 things come to mind:

1. use varying throttle while tuning it.

2. break it in the best you can with gaps in throttle, just so long as not extremely lean.

Any suggestions would be appreciated. I would lean towards (1) above until got within reasonable range, then (2), and fine tune it afterwards. This would indicate how important the etg and cht gages are in quick tuning analysis.

 

Break-in protocols shouldn't change with displacement. Make sure your jetting is not too rich either. You don't want fuel washing down the cylinder walls during break-in. It dilutes your engine oil and adversly effects seating the rings.