On the idle thingy,I have Jolly set so that the ammeter shows neutral-no charge,no discharge.Also,a 5 minute warm up is good,but avoid blipping the throttle just give it enough to keep it running.I like to warm Jolly until it is warmed,3-5 min.,then take it kinda easy for the first 10 minutes or so.The only thing wrong with my approach is that the bike may be getting a little sooty by the time I open it up to clean it out,but there is never any smoke,so this is what I do.I am a little cautious with this bike because,unlike you,I did not do a proper break in.I know that I cannot make up for it,just trying to do rite now.also,on shifting,higher shift points usually help any manual trans shift better.So,as you raise the speeds,the shifting will improve partly because of this and the other things mentioned.If not,the dealer needs to see about it.