De catted headers will give a noticeable improvement in low down torque. Fitting an end can will not give you anything else but a more fruity sound if that's your bag.
However, in my experience, if you have a non standard end can and remove the baffle, the performance suffers as I think the Boxer like some back pressure going on. Also, fitting a K&N without a power commander starts to seriously affect the fuelling which is probably why skid06 has problems.
So, changing the headers should cause you no problem. I've run Keihans for 67k and the bike runs great
Ilkleyal has it slightly wrong about improving the bike from factory standard. The factory settings are OK but once you have ridden a bike which has been properly set up without spending a fortune, the improvements are staggering