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 DiscThermostat Removal
Remove:
Fuel Tank (see Fuel Tank Removal in the Fuel System
(DFI) chapter)
Air Cleaner Housing (see Air Cleaner Housing Removal
in the Fuel System (DFI) chapter)
Throttle Body Assy (see Throttle Body Assy Removal in
the Fuel System (DFI) chapter)
Throttle Body Assy Holder Clamp [A]
...
Interlock Operation Inspection
Raise the rear wheel off the ground with the stand [A].
1st Check
Start the engine to the following conditions
Condition:
Transmission Gear → 1st Position
Clutch Lever → Release
Sidestand → Down or Up
Turn the ignition switch to ON and push the starter butto ...
Crankshaft Side Clearance Inspection
Insert a thickness gauge [A] between the thrust washer
[B] on the crankcase and the crank web [C] at the #3 main
journal to determine clearance.
If the clearance exceeds the service limit, replace the
thrust washers as a set and check the width of the crankshaft
#3 main journal.
Cra ...