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 DiscSpecial Tools and Sealant
Oil Pressure Gauge, 10 kgf/cm²:
57001-164
Oil Pressure Gauge Adapter, PT3/8:
57001-1233
Outside Circlip Pliers:
57001-144
Liquid Gasket, TB1211:
56019-120
...
Handlebar Installation
Apply a non-permanent locking agent to the threads of
the handlebar positioning bolts and tighten them.
Torque - Handlebar Positioning Bolts: 9.8 N·m (1.0 kgf·m,
87 in·lb)
Install the steering stem head with handlebars.
Install the washer [A] and steering stem head nut [B].
Tighten:
...
Rocker Arm Installation
Install the both rocker arms [A] so that their marks [B] face
left side.
Replace the tie-rod nut, rear shock absorber nut and
rocker arm nut with new ones.
Apply grease to the inside of the oil seals.
Tighten:
Torque - Rocker Arm Nut: 34 N·m (3.5 kgf·m, 25 ft·lb)
Tie-Rod ...