We've heard of stranger things...
We've heard of stranger things that call an airbox home.
Air intakes
Careless fairing removal and refitting can mean misaligned ram-air intake tubes that cause air leaks and a loss of intake air pressure. Make sure the ducts are properly situated into the airbox, and any hoses or resonator chambers are correctly fitted. It's also worth cleaning out any leaves, insects or small rodents that may have gathered in there. You'll be surprised at the things that can accumulate in these cozy conduits.
Ignition system
Standard spark plugs and coils these days are extremely good, and service schedules often leave spark plugs for 12,000 miles between checks. But they don't last forever, and small deficiencies can cause slight misfires at high rpm that cut power.
Pull them out and check for cracks in the ceramic insulation or oil/water in the spark plug tunnel (this can cause spark tracking).
If the bike's fueling (jetting or mapping) isn't perfectly set up this can wear down the life of a spark plug as well. Some fine grit sandpaper can help freshen an old plug, but ideally you'll replace them with the recommended OE plug-not cheapies from Autozone!
Dyno
The best way to know where you're starting from is to get your bike to a dyno. A good dyno operator will be able to tell you if your bike is down on power, and looking at the printout may give pointers towards problem areas such as high-rpm misfires, flat-spots or spikes in the power. Before and after runs will prove whether your hard work and dirty hands have paid off.
Brakes
Your brakes are there to stop you. But if they're neglected, they can bind and drag which will soak up your precious power. Put the bike on a rearstand or get a friend to lift it up onto the sidestand, and try spinning both wheels (one at a time). The rear will obviously have some drag from the chain (if you can, loosen the adjusters and lift the chain off the sprocket beforehand), but the front should spin pretty freely. If you feel any drag, then give the brakes a fettle. The steps will vary between bikes, but essentially you need to remove the pads, push the pistons back in, and clean away all the dust and grime in there. Pump the pistons out a little to make sure they're clean, and push them back in before putting the pads back in.You've seen how filthy the front wheel gets from brake dust, so you can imagine what the scale of griminess is inside the caliper. Get in there and clean.
Oil and filter change
Shame on you if you don't do this regularly yourself. Old, tired engine oil can sap power from your engine as well as accelerate the wearing process. The friction-reducing additives in modern oil degrade over time, so dumping the gloopy black muck out and replacing it with fresh, golden multigrade can gain you a couple of horsepower as well as make your motor last longer. Plus you can enjoy a sense of accomplishment after completing the task.
Swapping to a thinner race oil can give even more power gains by reducing friction and pumping losses, but you'll need to change the oil more often.
Throttle cable adjustment
Is your throttle cable adjusted properly? If the throttle valves aren't completely open when the twistgrip is fully turned you'll never get max power out of your engine.
Get access to the engine end of your throttle cables where they operate the pulley that turns the butterfly valves inside the throttle bodies or carbs (you may need to take your tank off or remove a side panel). Make sure that when you turn the twistgrip fully back the pulley is turned completely so that the butterfly valves inside are perfectly parallel to the airflow inside.
There are normally cable adjusters near the twistgrip and the pulley, and if you need to take up any slack or free play simply make minor adjustments at both ends.