Mark, You need to pay more attention to the model numbers posted. The manual link you is for a different older model.
John Deere E110 Service Manual
As for the brakes you basically just sure you see the spring compress when the brake pedal is depressed.
Second according the IPL there is no roll pin on the brake linkage that connects to the transaxle. They used a Rue Ring clip.
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Depending on how much you have been using the brake it might worn out inside the transaxle. I would recommend carrying the mower to someone with experience with hydrostatic transaxles.