Here in Australia you can only download/upload a stage 1 flash using a Supertuner pro ( $650 to buy , "marries" the bike's ECM !)
You should have been given that with the bike at purchase ( they can and do "go missing" in the bike's life journey)
OR it may have been flashed with a shop using Power Commander Licence to do a one off flash. Unlikely AKA impossible in Australia way back then.
There was a system for a while whereby HD dealers used a one off cartridge in a dealer digitech computer to reflash a stage 1 calibration. ( last used 2006/7 !)
So could be that scenario with your bike. Any changes / reflashes now will need a Supertuner pro ( or one of the other flash tuners like TTS or Powervision)
Probably $650 whichever way you go.
Where in Australia are you ?
Mate , 2005 there are no O2 sensors to worry about.
Plus the original SE slip on mufflers were really quite free flow and almost straight thru' in any case
I don't reckon you'd have any dramas with those true dual replacements.
They may "pop" on decel a bit , I tend to find that they do
I'd be giving it a try before dropping $650 plus on a tuner you'll only need once as you say