On a much older thread in the days of the LGR, I believe either Mooncoon or tiriaq transcribed a discussion with someone at the CFP - where they stated the breech plug was the "firearm" for registration purposes. Although as vagrantviking linked, certain guns will be different than others, depending on their specific construction.
As to your more specific questions? I'd say that changing the lock would probably be fine, reboring or relining the barrel absolutely - replacing however starts to get into the iffy zone.
I would agree to just get a repro flintlock or preferred mechanism if you can, of course if you are thinking pistols this is out of the question