During our trip in fact the police never stopped us. We tried to keep a low profile, but for two strangers on a tandem this is not easy. Nevertheless we had no problems. We adjusted to the traffic rules and used the sidewalks whenever it was feasible or necessary. The traffic in Japan is well behaved, but sometimes the roads are narrow or busy.
Sidewalks can then give a good refuge.
A problem remains riding through tunnels, especially the old ones have little space for bicycles and have bad lighting. Sometimes there is a narrow path on the side, but one has to be careful. The cars make a terrible noise and seem to be crashing down on you all the time. We sometimes choose the detour over the mountain to avoid the tunnel, but often that meant much more climbing to do. In one case we came through a brand new tunnel, specially constructed for cyclists.