If a master cylinder or piston shows any damage, replace them.

If a cup is worn, damaged softened (rotted), or swollen, the piston assembly should be replaced to renew the cups.
If fluid leakage is noted at the brake lever, the piston assembly should be replaced to renew the cups.
If they are damaged, replace them.
If the springs are damaged, replace them.
If the relief port becomes plugged, the brake pads will drag on the disc. Blow the ports clean with compressed air.
Front Master Cylinder [I] Rear Master Cylinder [J]

Rear Master Cylinder Installation
Brake DiscAir Intake Duct Assembly (Other than US, CA and CAL Models)
Install the seals [A] as shown in the figure.
Fit the projections [A] of the air intake valve to the hole [B]
of the air intake ducts.
Tighten:
Torque - Air Intake Duct Assembly Screws: 1.5 N·m (0.15
kgf·m, 13 in·lb)
Hang the shaft [A] to the air intake valve securely ...
Check 3-6: Neutral Indicator Light (LED) Inspection
Connect the leads in the same circuit as Check 3-2.
Connect the terminal [8] to the battery (–) terminal.
Check that the neutral indicator light (LED) [A] goes on.
If the indicator light does not go on, replace the meter unit.
...
Connecting Rod Big End Side Clearance Inspection
Measure connecting rod big end side clearance.
Insert a thickness gauge [A] between the big end and either
crank web to determine clearance.
Connecting Rod Big End Side Clearance
Standard: 0.13 0.38 mm
(0.0051 0.0150 in.)
Service Limit: 0.58 mm (0.023 in.)
If the clearance exceeds ...