They SHOULD work just fine, the Customs & Heritages use the same header and brackets, it's just the mufflers that were different. Are the pipes on-line? Can you send a link so I could see them, just to be sure?
The older Screamin Eagle pipes were not that great for performance, they sound ok, but the baffle design isn't much better than stock. You would actually get better sound and performance out of a simple set of Cycle Shack pipes from Drag Specialties.