Generally aftermarket filters have more airflow than the stock units, so more air without changing jets will make the bike a little more lean.
(This is mentioned in that link i showed you) You mentioned before that you changed your plugs and saw the coloring on them.....looking at plug color to diagnose how the engine is running only works if you hold the engine at a constant rpm for 10-15 seconds and then kill the engine and immediately pull the plug. If your engine was idling for 10-15 seconds prior to you shutting the engine down before you pulled the plug, all you were diagnosing was idle fuel mixture.
About tire pressures on a bike, it really depends on what you primarily use the bike for. Lower pressures will give you more cornering grip, but more resistance. Also, the steering wont be responsive. With higher pressures, the steering will feel light and snappy, but cornering grip is reduced slightly (this only matters really if you are on a track....racing....)
On my ninja 250, since i primarily use it as a commuting bike, i have the pressure set on the most the tire can handle (i think its 44psi, around there).
Changing the gearing will help. On my ninja im at about 6800rpm at 70mph, and thats after i geared it down!
Stock, the bike runs at about 8500rpm at 70mph.... Your bike's acceleration will decrease if you gear the bike down, so you need to consider what you want to use the bike for (fun, economy, or both
)
Here are some sprocket options for your bike. Try going up 1 tooth in the front and see how you like it. Its cheaper and easier to change the front sprocket than the rear.
JT Front Steel Sprocket at BikeBandit.com