Years ago, I watched as a section of a Kumamoto Castle wall was restored: Each stone was numbered and the wall was photographed before being dismantled to ensure that it could be properly reassembled as each stone had to fit in a particular position like a puzzle piece.
Imamura Katsuhiko (76), former head of the Kumamoto Castle General Office, says that the key to restoring the walls is to analyze old photographs and collect experts from around the nation. He also notes that the work difficulty is compounded by the different construction styles used in the various walls - and that that in itself is what makes Kumamoto Castle so historically valuable.
The current administrators of the castle are struggling to secure photographs and records of past restoration to enable this, and a search is on for masons with appropriate skills. I suspect that restoration will eventually result in a use of original and newly-cut stones, particularly as many of the original stones were broken during the collapse. However it works out, this will likely be a decade-long project. - William