Question #1 - TuneBoy is a software program that allows you to adjust most of the settings, such as fuel, ignition timing, idle settings, speedometer settings, etc. in your bike's ECU. and yes, you use a laptop and the TuneEdit program to make the changes. It is not an add on like the Power Commander or F2000. How the bike runs after you make changes with TuneBoy depends on the changes you made. It's a great program and diagnostic tool as well, but it also leaves you alot of leeway to screw things up if you're not atleast somewhat knowledgeable about your bike and computers.
My personal opinion is that you would be pretty happy with a drop-in K&N filter, plus TORs or other aftermarket exhaust, and the appropriate Triumph tune to match.. then just take off and ride..
That's the combo I run at the moment on my RIII.. fixing to go the Jardine route here shortly though...