NEXCO Central sells passes that let you drive within a set area for a flat fee. It also runs a discount plan for motorcycles only. The more you drive inside the area the less each kilometre costs, and used well it comes to far less than paying the tolls. Plans come and go, and each must be applied for in advance.
The ferry links Irago (Aichi) and Toba in about an hour. Motorcycles are limited to ten per sailing; bookings are taken by phone from three months ahead until 16:00 the day before. Without a booking it is first come, first served, and sailings are cancelled in rough weather.
Before boarding you sign a lashing consent form and hand it in at the ticket window when you buy your ticket. Forms are at the pier counter, or print one from the official site.
On board the crew secures your bike with lashing belts and chocks so it does not fall over. A bike they judge cannot be secured may be refused carriage.
Check your bike as you board and as you leave. Damage reported after you have left the ship is not accepted. On a return trip the same form covers the way back.
No bookings are taken over Golden Week, Obon, the Respect for the Aged Day weekend or New Year. In those periods the only option is to reach the pier early.
Both shrines have somewhere for motorcycles, though the arrangement differs. The official sites do not say, so it is set out here.
Where motorcycles go changes with how busy it is. Follow the directions of the marshals when you arrive.
Motorcycles with a sidecar park in the municipal Naiku lots on the same terms as cars. The Jingu Kaikan car park takes four-wheeled vehicles only.
Over the New Year period, Golden Week and Silver Week, traffic restrictions apply around the shrines. Motorcycles are exempt from most of them, but not from the Ise IC exit closure.
On the days Ise IC is closed, Ise-nishi IC still lets motorcycles off. As the park & bus ride does not take motorcycles, ride straight to the shrine and use the parking above. Dates and hours change every year, so check Rakuraku Ise-Moude before you set off.
The car page explains each restriction in detail.
Two roads here are touring classics.
Ise-Shima Skyline
A toll road over Mt. Asama from Naiku to Toba. Motorcycles pay ¥900; bikes of 125 cc and under are not allowed. The summit car park has room for 20 motorcycles.
It opens in the morning and closes in the evening. It is shut overnight, so check the hours on the official site.
Pearl Road
A 23.8 km prefectural road from Toba to Shima, running through the hills along the coast. It was a toll road until 2006 and is now free for its whole length. Being an ordinary road, it has no engine-size limit.
Partway along, the Toba Observation Deck has free motorcycle parking.
Both are winding mountain roads with blind corners. You will be taking bends without seeing what is coming, so keep your speed down.
Sights
Eat & shop
Listed only where the source states something about motorcycles. A place not listed here simply has no information either way.
Visiting all 125 shrines means going to 55 places, and only 3 of them list any parking. In a car you spend the day looking for somewhere to stop.
A motorcycle often finds a spot where a car cannot. Park where you are not in the way of the shrine or its neighbours.
Buses and taxis work too. Buses are infrequent, though, and they fix the order you visit in; a taxi costs you at every stop.