As shown in the diagram you posted, the two hot wires from the circuit breaker/switch/timer/automation system get connect to terminals L1 and L2. They didn't show it in the diagram, but the green ground wire from the circuit breaker/switch/timer/automation system also gets connected to the green tinted screw on the pump chassis (in the lower left corner of the opening in the picture of the end of the motor you posted).
By the by, the WhisperFlo WFE-6 pump is a 1.5 HP, not a 3.5 HP.