Just to add my experience to this thread:
1) the valve clearances had a lot of effect on the ability of my NTX to pull from lower RPM smoothly. From the factory the bike came with 0.004" and 0.006" and on the first service, which I did not do myself because it was included, they also set it to the same as per the sticker under the seat, and I forgot to tell them to do 0.006" and 0.008". So I put about 2K miles on it with tight clearances and then reset it to world spec. Very noticeable difference, in the low end smoothness and in how the bike behaves in 6th gear under 5K. Before that I never used 6th gear at all, now I often find myself in 6th under 5K RPM on the freeway and it feels smooth.
2) a better flowing exhaust does flatten out the torque dip from 3K to 5K substantially so this will help running lower RPM in high gear also. The curve supplied by, say, Mivv, for their Speed Edge exhaust as tested on an NTX, is EXACTLY how the bike feels after such an upgrade. When I had the 8V Griso, Todd's pipe also produced the exact same positive effect on midrange torque.
3) it improves as it breaks in.
Of course, a proper tune is a must -- throttle body sync as exact as possible and TPS reset. My NTX had the biggest torque dip/lean stumble/vibration/whatever it really is right at 4K RPM sharp (MUCH less so after the pipe upgrade) so I do the high RPM sync right at 4K and it smoothes everything across the range. A good indicator for me aside from how the engine feels is whether I can see clearly in the mirrors at typical running RPMs -- and when the bike is tuned well, I can, and have no complaints about the stock mirrors...