Yes they will work. HD is telling you no because the SC are street legal for bikes with cats in them. But they will bolt right up, no problem. Just be aware, your bike will be really loud, so if you aren't looking for that, don't do it. YMMV though.
Put these on my 03 ultra 88", screaming eagle stage 1 air cleaner and a PCIII. Sounded like hammered hell. Took them off after 40 miles and sold them. Dealer also told me they would fit my 03. Heard these on a 103" motor and they sounded great, not so much on my 88"