Wirelessly posted (blackberry: BlackBerry9650/5.0.0.699 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/104)
I also primarily use amex, have visa and mc as a backup.
I have been in tokyo for 4 or 5 weeks now (also traveled to kyoto).
Have not needed to use non-amex yet, with the exception of many restaurants whom accept credit cards only for dinner (that's right, I've been multiple places who gladly take my cc for dinner but refuse for lunch).
Atms here are a different story though, my schwab card has -only- worked at 711 atms. I have tried it in literally dozens of others.