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Every new project brings a whole area of information that you never knew existed. As I was starting to learn about my new 1966 Honda S90 I was somewhat surprised to find out that my bike has some different types of screws and bolts on it. Many thanks go out to the folks on the Yahoo S90 list for providing most of the following information.

Prior to 1967, the Japanese had their own system of bolt threads, defined under a JIS (Japanese Industrial Standard) standard. Most of these bolts were the same as what we now know as a metric thread, but not all of them. In 1967 the Japanese adopted the ISO (International Standards Organization) standard for metric threads, changing the few sizes in their old standard that were different.

Honda used the JIS standard up until around 1967, when they switched to the ISO standard. To quote a Honda service bulletin from 1967 (TL #27, June 8, 1967):

This change-over will be effective from the start of production of all new motorcycle models first produced after the beginning of 1967. In all other models, those previously in production, the change-over will be made gradually and on no set schedule

This means that any existing bike line (such as the S90) was changed over to the new thread system gradually, most likely as existing stocks were used up. Bikes prior to 1967 (such as my 1966 model) will use the old thread system, while any bike 1967 and later could possibly use either one. The only good way to know what your bike has would be to check the threads with a thread gauge.

The change from JIS to ISO resulted in some differences to the bolt heads, but the most important change for anyone working on an old Honda is that the thread pitches for some sizes of bolts changed as well

DiameterOld JIS thread pitchNew ISO thread pitch
3 mm0.60.5
4 mm0.750.7
5 mm0.90.8
12 mm1.51.25

This change has a very important implication for early Hondas:

Modern ISO metric screws and bolts are not the same size as many of the fasteners on our bikes!

Specifically, the tank badges use the 3 mm screws, and the 5 mm screws show up in all sorts of places. I have not found a good source for these yet, so it is critical that you take care with any fasteners you are using on your bike, as they may not be replaceable. Using a modern ISO metric fastener in place of a JIS fastener will probably cause issues including stripped threads and poorly fastened bits. Fasteners in sizes other than those listed in the chart above were essentially unchanged by the switchover, and can be found at any good local hardware store.

I've been told that the proper taps and dies are available at Sears, but haven't followed up on that tip yet. Having those handy would help to fix any prior bodged repairs, and might just work to save a partially stripped JIS screw.