Yes, all HD bikes since '02 use Delphi ECM's.
My personal preference, in order, would be:
1.) TTS Mastertune w/Cables
2.) SEPRT (NOT the street legal version...the Pro Tuner)
The TTS has more functionality, and is becoming a tuning device that many independent shops use. The best advice I can give you is to first find a good tuner in your area, and find out which tuning device they prefer using. If you will ask here on the site, someone will likely be able to recommend a good shop in your area that uses either of those devices (again, my preference being the TTS). I personally am not a proponent of devices that piggyback, or that replace the ECM. IMO, it is better to change the program in the stock ECM. With the TTS, you can save a copy of the stock program so that you can always go back to it should the need arise. Replacement ECM's give HD a really good excuse to deny warranty coverage. It would be like buying a new computer from Dell, changing the motherboard out, then expect them to warranty the computer.
If it was me, I'd replace the entire exhaust system, then get a good tune and just ride it. The difference over stock will be significant.
Technically, you might not need any tuner at all with just slip on mufflers. However, even a stock bike can benefit from a good tune.