I joined this SE because I see the death of guitars.SE as practically inevitable.
Will there be some form of reputation migration from other sites as they are folded into this one?
Yes. If your account here and your account there are linked, your questions and answers will belong to you if a question is migrated (along with the rep you got/lost from them). When Guitars is closed, the StackExchange people will do their best to ensure all the questions moved here get assigned to the right accounts. Again, this should be no problem if your accounts are linked. Otherwise, just speak up before it happens (there should be an announcement) and they can get things resolved.
If something gets messed up, just flag the question or answer and ask a moderator to fix it (if they can't, they can contact the overlords). It's much preferred that you have everything straightened out beforehand, though.
There's a post on meta.guitars that talks about the upcoming merge and what will happen: http://meta.guitars.stackexchange.com/questions/136/announcement-save-guitars-se-by-supporting-the-music-proposal