Dear James.
It is not entirely unusual to have gold menuki, what you do next is of course up to you. I would love to see a picture of the entire koshirae but the really nice wrap is going to need redoing and you need to find someone who can do it justice. While this is happening you could remove the menuki and replace them with similar shakudo examples. For me the decision would hang on whether the koshirae was original or not, I note that it does not seem to have seppa, do you have a feeling that this has been put together or perhaps the tsuba has been swopped out? The tsuka appears to be original and attractive so my perspective would be re wrap just as it is including these menuki.
Dealers and collectors have always been inclined to swap fittings, more money to be made selling the boxed fittings and putting together a koshirae. Personally I would regard that as heresy and would want to retain anything original about the sword. If the seppa are indeed missing then you might have to change the Namban tsuba for something thinner, add seppa, and that would change the dynamic somewhat.
Looking forward to a picture of the whole thing and what others have to say.
All the best.