Agree with Mr. Schmidt that the Yoshi 3/4 is THE way to go on the exhaust choices mentioned. I've tried both bolt-on's and 3/4....no comparison.
Taking off the airbox top along with the snorkel DOES change the airbox tuning, and can influence throttle response and torque production down low to midrange. The snorkel really isn't a restriction...and plays an important part in box tuning, so if you're looking for strong midrange (with good bottom end too) my opinion would be go with stock box and K5-7 short snorkel w/K&N or BMC filter. I've done back to back testing of the filters and my bike runs better with the more flexible K&N for some reason besides restriction....which the stock filter doesn't have a lot of. But it's night and day more powerful and gets better gas mileage with the flexible filter installed.
If you take off the top, be prepared to tune around the loss of box resonance....which can be done, it's just more work and you can leave the tune closer to stock if you don't mess with the box resonances.
And.....last but not least, removing the STV's gives a performance boost that many/most people enjoy once they've tried it. Some find no difference, but it's worth a try if you desire better response.