If it's a straight through pipe from the standard set-up, chances are (like mine was) it'll be running rich. (If you're getting lots of pops/bangs/flames when letting off the throttle between 5k-3k then it certainly is)
If you want that extra 0.5bhp then feel free to put in a race filter before you get the ECU mapped, but depending on which set-up you get, will depend on if it'll make any difference or not;
If you're paying £300+ for a full set-up with a power-commander, then it'll make a difference.
If you're doing what I did and paid the £60 for a Yoshi set-up on the stock ECU (which only allows +/-5% alteration on the fuelling) then adding a race filter won't make much difference.
As for running the engine for that length of time... depends what sort of mileage you do. If you only do the odd bimble here and there, it's not going to make much difference. If you commute 200 miles a day on it, I'd keep it at home until you can get it mapped!
Hope that helps!
Ps. My idle speed also dropped after fitting the system, causing a few stalls - just alter the idle-speed screw on the left of the bike (Let me know if you can't find it, not obviously until you've used it) and set it back up 1.4k rpm.