I've only been able to really experience this issue at night time, when it's around 60 or so degrees out, but while riding after about 9 or 10 miles, it will sometimes feel like I'm not getting much power. The best I can describe it, is it feels like I'm in too low of a gear, when I'm only around 3-4K RPM. Just feels like it NEEDS to shift. If I shift, it seems to go away until I get back into that RPM range. Almost like the engine is working harder than it normally does, but is only within the above stated RPM range.
I've noticed the bike temp is usually around 174 to 180-something, not sure if it is relevant.
Could this be a missfire taking place? Possibly a gearbox issue? Couldn't be clutch, right? The only changes I've made recently was I changed the clutch cable, but it doesn't seem to do it during the day.

About 17,500 miles on the bike.

 

Do you ride your bike hard? Or do you baby it more?

What RPM range do you normally operate in? Under 5k on average?

 

I'm a newer rider, so I haven't even gone on the highway yet, just been riding for about 400 miles or so, all been sidestreets, usually around 3-5K, mostly under 5 though, yeah.

 

So, what i was told was by the mechanic at the local dealership was the f4i was not designed as a commuter bike as like around town put put kind. It was the supersport of its time. And is a high performance engine. So it has to be ridden hard, otherwise the engine gets "charged" as he called it. Carbon buildup and other contaminants aren't expelled when ridden "easily". I noticed power improvement when i launched a little harder and rode in a lower gear. Not always, maybe once or twice a week. Try it out and see if it makes a difference.

 

Looks to me that you are riding in low rpm range, 4 cylinder engines need to rev to generate power/torque.
Keep rpm above 5k for smoother power output, rev it up to 7-8k once in a while to keep things running smooth.
Steady throttle at low rpm range will usually present poor fuel delivery problem more pronouncely.

If your fuel delivery is clogged up already, you might need to run it with Seafoam w/full tank of fresh fuel, ride it aggressively let the engine rev, accelerate hard to clear up the gummed up injectors.