Kmutt,
A slip-on should help a good bit. Removing the secondaries and cleaning up the throttle bores and blades will likely improve output at higher rpm. As will using the larger throttle body from a normal R3, and adding individual filters under the bear claw. But the larger throttle body bores will likely lose a bit of torque at 3000 rpm and under.
Every R3 I have tuned wants a bit different fueling, but the timing requirements for max brake torque (MBT) seem to be very similar if using the exact same bolt-on parts. The difference between loading a downloaded tune, and having the bike tuned well, can be seen in the above graph in the yellow and green lines. This only shows output at WOT, the differences at part throttle can be even larger.
As you can see in the green and brown lines, tuning for the specific fuel you use regularly is important on the R3T - smaller bore bikes are less sensitive. If you run 87 or 89 octane, tune for it - preferably the same brand you use most. Lower octane fuels tend to improve output at lower rpm, and increase throttle response. Using higher octane (93 pump premium) tends to improve higher rpm output, and will lose a bit of low end torque and throttle response - unless tuning is optimized for this fuel.
As you add modifications that improve airflow into, and out of, the engine, the cylinder pressure will increase. This means the engine will demand more octane for best performance (even if the engine is not knock limited, like in the case of the R3T).
I hope this helps,
-Wayne