If replacing the rod itself (e.g., the rod that is "stuck" in the piston) you need a special tool to release the retainer clip. The retainer goes between the rod and inside the piston to prevent the rod from slipping out if the master cylinder or brake pedal comes loose.
If you do not have the tool, you can try inserting a small pick to bend the clip outwards away from the rod and pull the clip out later after the rod is free. Some people have reported banging the rod with a hammer to break the clip, but will certainly distort the eye hole of the rod.
Most people avoid trying to get the rod out and buy an adjustable rod - especially if doing a single to dual master cylinder conversion.
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