Dave, I'm not sure of your experience level here but if you are scientific (whether trained or self taught) you should familiarize yourself with you are trying to do or want to accomplish. You have a couple of options before you go the route of getting the autotune as I see it. Also the autotune is not as "auto" as it sounds.
First, you can get a wideband sensor and meter/data logger and start gathering data on your AFR at RPM vs throttle position. This will give you what you need to do to the fuel curve and settle the "how do I know...". As for the "how much do I back it off", well that is trial & error with many repetitions. This is what all "tune guy's" do, you make a run, analyze the data then tweak.
The second option and I know you're not going to like it... is to find a reputable tuner to take another shot at it. It's no doubt the first guy you went to had no clue but if you do a search I'm sure you can find one within half a day's ride. This will give you a better starting point after which you can then data log your rides and see what's happening.
Most importantly I would suggest first setting a zero map and make sure your bike is running in top shape, you'd be surprised how often people try tuning out basic mechanical issues (spark, vacuum leak, and fuel delivery issues) then only end up totally frustrated. You said you have the slip-ons and yes, no, maybe, a K&N filter as your mods, well if so there is no reason your bike should not run well with a zero map (it won't be top performing but it should run well). If it doesn't maybe there are issues, either mechanical or your PCIII is the problem, these things should be ruled out first before proceeding in order to achieve your goals.
