Typical tuning procedure goes in this order:
1. lock in your mains for WOT/high-end 1st
2. adjust mid-range with clip position
3. dial in idle & low-end with pilot & mixture screws
Trick is figuring out which way to adjust and where.
Old-fashion method is just doing runs out on road and recording elapsed-time for 0-60, 60-80, 80-100, 1/4-mile, etc.
Another method is audio-recording and using a desktop-dyno package to analyse. It times acceleration and can give you semi-accurate dyno-charts and ET time-slips.
if your wideband has datalogging, that would be best. Not safe trying to stare at AFR gauge while going down street WOT. Give you most accurate tuning-data. Aiming for 13.5:1 in high-end gives max-power. Little richer in mid-range gives smoother transistions.
I suspect that your 5k-rpm stumble might be lean, can adjust clip to raise needle to see if it improves. Otherwise go other way.
Appears MotionPro lost interest in Ninjette kits when new-gen came out. They never developed new-gen needles for stock bikes. Their kit appears to be geared towards big-bore bikes with cam upgrades. Does nothing for stock bike. Note that lots of people resort to jet-kits to compensate for dirty clogged carbs.
interesting dyno-charts and upgrade progress here. Tyga full exhaust gives about +1hp advantage over AreaP.
http://www.racingorder.com/?s=dyno