As Bill said, it is best to log everything. In certified aircraft, it is harder to get away with some things because they have a TC the must be complied with or have documentation of any departure from the TC, where an STC or other 337 requirement.
An experimental is different in that there is not document that says exactly how it was originally configured, so it may not be possible to determine that some changes weren't original. The same rules still apply, though. The more you document, the more the plane will be worth as it ages, IMHO. When I do a Prebuy, seeing a logbook entry for a bolt being replaced or a nicked filed out of the prop or a swapped alternator shows me a good attention to detail by the owner/mechanic. No entries between condition inspection entries give me less confidence, although some times there is nothing done between inspections, but more often than not, probably, there is.
An alternator swap is beneficial to you and any potential buyer because there is documentation of how old it is and how many hours are on it. The nick in the prop is the same way.