You can do what I did if you can stand the wait....wait till the 12k service and have it done then. That service is very expensive mainly due to valve adjustment. This way you don't need that since the new top will include valve adjustment. So do any other stuff lie coolant change or whatever yourself, and the cost of the service is basically replaced with the cost of the kit and labor, which brings the kit cost down to about $1000 or less depending on your dealer's labor cost.
And yes, get the pipes right off. They will make the bike's power much more tolerable w/o the BB kit. I have the short tors and for me i felt they too the power to a point that i felt comfortable with the power. Before that i felt i was always wanting more chronically. As to what pipes, i am a big purveyor of the short tors for a number of reasons...they're by far the cheapest, (1/2 as much as hogslayers) they really bump up the power as nicely as any pipe likely will, somehow they actually reduced the bike's vibration, (i think due to the length and the resulting pulse length) they look great, they allow access to the rear axl and for easier wheel cleaning. I also don't like real loud pipes, but i do like a bit more than stock, just enough to hear it. The short tors do just that, so if thats what you like they are going to be quieter than the hogslayers or any other pipe that removed the cat. Anyways, some of that is subjective so it's your call, but I find them absolutely perfect.