Shikoku Henro Trail has ten routes. And you can complete each route for two nights.
Since you will come all the way to Shikoku, why don’t you put a few routes together during your trip?
Here are five recommended combos based on the difficulty level and the ease of the transportation in between.

A. Tokushima Course
Distance: 110.5km
Difficulty: Beginner to Intermediate

Route 1: Introduction to the Shikoku Pilgrimage
Route 2: Experience Tokushima’s Attraction 

After completing Route 1,  take Tokushima Bus(Kamiyama Line or Sanagochi Line) from Kamiyama Spa-mae(Kamiyama Onsen-mae)to Tokushima Station (Tokushima Eki-mae) . Stay overnight somewhere near the station. The next morning, start off by bus from Tokushima Station to Doll Cultural Exchange Center-mae (Ningyo Bunka Koryu Kaikan-mae on Katsu-ura Line) and proceed to Route 2.
B. Kochi Course
Distance: 125 km 
Difficulty: Elementary level

Route 3: Sea, Mountain, and Village in Kochi 
Route 4: Fully enjoy the Pacific Ocean

After completing Route 3, take Tosaden Kotsu Bus (Line S2  or S9) from Nagahama to Kochi Station Bus Terminal. Stay overnight somewhere near Kochi Station. The next morning, take the JR Nakamura Line from Kochi to Tosa-Saga to start Route 4.
C. Ehime Course
Distance: 133.5km 
Difficulty: Intermediate to Advanced

Route 5: Walking in the opposite direction on ancient paths of the Shikoku Pilgrimage 
Route 6: The Golden route in Ehime

After completing Route 5, take Uwajima Bus (Jobe Line or Shukumo Line) from Iwamatsu Shutchojo to Uwajima Eki-mae, and then take the JR Yosan Line from Uwajima to Matsuyama. Stay overnight near Matsuyama Station. The next morning, take JR Shikoku Bus (Kuma Kogen Line) from Matsuyama to Kuma Chugaku-mae to start Route 6.
D. Kagawa Course
Distance: 135.5km
Difficulty level: Intermediate

Route 7: The area associated with Kobo-Daishi 
Route 8: Kagawa Last Eight Temples

After completing Route 7, take the JR Yosan Line from Zentsuji to Takamatsu. Stay overnight near Takamatsu Station where there are many accommodations. The next morning, take the JR Yosan Line from Takamatsu to Kokubu to start Route 8. 
E. Cycling Course
Distance: 417km
Difficulty: Intermediate
9:Cape Muroto Cycling Route
10 :Cape Ashizuri Cycling Route

The distance between Route 9 and Route 10 is more than 100 km. You can bike the whole way or switch to the JR train. If you take the train, stay overnight near Kochi Station after completing Route 9 and move from Kochi to Nakamura by the JR Yosan Line the next morning.  You can bring your bike in a bag to the train. A bike transport bag and a bike are available for rent at JR main stations. Please inquire for details.