Bribe36, do not get pulled into the Harley Lore. The best thing is to discuss what to do with several tuners. IMO the best thing to do is program the ECU on the bike. There are many tuning software packages available now that will tune the ECU on the bike and done properly the heat will be reduced, there will be snap back in the throttle, No pinging and a very smooth and rideable bike. I am a tuner and even the stock as delievered bikes form the dealers can be improved with a proper tune. Prices vary by region so contact some tuners in your area and ask for pricing.
The biggest single effect on a bike is an exhaust change. Any changes in exhaust flow will effect how the bike runs and rides. I worked on this with Texas103 and ask him the effects we saw. This will effect the AFR tuning the most, add a free flowing air cleaner and it changes it even more. The closed loop system will compensate to some degree but will not compensate in many areas of the VE tables or fuel map. Most customers I have want the bike tuned for all areas and not just the area that is closed loop. This is what I have seen from many bikes I have tuned.