hondy gearboxes get a little notchy when then come up to operating temp. As for the cylinder backfiring or cutting out that is not normal. An overheating honda tends to detonate...a lot. It will sound like pebbles in a coffee can when you first let out the clutch. It could be that your ignition timing is off and causing overheating and backfiring. It could also be fuel delivery. As for the idle quality, you are supposed to set the idle when the bike is warm, which means that if you set it when it was cold then as the bike warms up the idle will drop, if it was low to begin with it will stall.