ok, "runs fine" may be a subjective reference but I believe the sentiment is: "idles normally and smoothly, accelerates and decelerates without hesitation and popping, starts quickly and shuts off without engine run-on". GRC, Haird, 2k, timo, Ken and a bunch of other guys can give you a more complete description of "runs fine" if necessary. The point was made that dankwiz just wants to "get by" for a year without dropping a lot of cash into a bike he fully intends to trade, he wants to use it, but he doesn't want it to sound "stock" either. You sound like an experienced tech old_dirt, surely you would agree he won't damage the bike with a set of slip-ons and although he won't obtain remarkable performance, he can ride until the 2015's come out.
As far as the cat observations, the main thing I noticed when I switched headers was less heat. But I agree, several guys have gutted their stock pipes, but I have never read a post where that was the end of it, they all received additional tuning. But if you want to kick that around, post the question in "intake, exhaust, etc" and discuss it there, we have some incredibly experienced people here and I'm sure they would enjoy discussing it with you.
OWL
Owl, you are basically correct, but 'won't hurt the bike' is kind of a sideways answer. If the OP rides that average of 5k a year? Prolly not. If he is an experienced touring rider and will do 20-25k on the bike... then... I would like to differ. Running over a point AFR extra lean will, at some point, come into play. I'm thinking of the next owner, here.
If the op wants to keep the bike low mileage, and putts around and doesn't actually 'tour' on this bike... I TRULY hate to say this... put a set of XIEDs on the bike at a minimum. Sell them for 50% of cost next year. IMHO, XIEDs are not any kind of 'solution' for folks, but they will beat a blank for a short term ride. (Keep the throttle and RPMs down low).
Owl, I'm kind of a nut. AT different times, I have ridden my bike with twin PCs strapped on and have recorded both WB and NB info for tuning. Bike looked like a science project with the vacuum pump strapped to pass board, etc. Then... I became more serious as I find tuning and LEARNING very rewarding, I bought a Dynojet 250i. I like to try to give the 'bottom line' at all times AND help anybody. Scientific method simply can NOT involve a single bike with a single rider upgrading bikes with a butt dyno, IMHO. We ALL do it, but doesn't make it right, either.