I have a 2010 ultra classic and have put on the rhinehart slip ons and soon to install a se stage 1 intake kit. I have done research and to the best of what i am understanding you have 3 options to get your bike tuned.
1. you can have the dealer reflash the ecm with a stage 1 tune that is specifally designed by HD to match the bike and their SE parts, but most dealers say that this tune will work for most mild mods since none of them really differ much in the performance areas, mostly cosmetic and sound differences. all of them increase air in and exhaust out. therefore increasing power and requiring a non-stock ecm tune, I beleive the dealers call this a ecm download and should run ya about $150-180 at the dealer. good if your done with mods and want a mild setup.
2. you can buy the SE street performance tuner which is about $320 and this will allow you to take it to HD dealer and they can download a HD map to your ecm and only charge about $50 bucks. there are some larger deales that actually have dynos that will sale you a map for this unit that is more specific to your setup for about $50 also. this option would be good if you plan to make small changes over the life of the bike. but would require hd dealer to download a new map after each change.
3. the most costly up front, is the SE pro race tuner and software. this would allow you to not only download stock hd maps for your setup, but also allow you to use the autotune feature to get a closer tune to your setup, or take it to a dyno shopp and have them custom tune it to your preferences, such as full race tune giving the best power but least efuel econ and very high heat. etc.
i am still trying to decide which way i should go. i want a good tune to cool the engine down and accomidate the intake and pipes, but want the functionality for the future if i decide to go big bore or cams. etc. just depends on what you want and how much you wanna spend. if i am incorrect in any of this please let me know as it would help my understanding alot.