Hey bill, it's rare to see webmasters from Osaka around!
Like you said, since Google also provide the algo for Yahoo and other local search engines, they control the vast majority of Japanese search queries...
5% is huge because most of the sites affected are commercial ones (like "buy #*$!" or "#*$! services"). It would be more like 60-80% of commercial queries affected, which represents 5% of total queries.
I saw major changes for all the keywords I am following, some low quality sites just disappeared and rankings moved a lot (and keep moving a lot) in general.