I wouldn't have bought this timer had I known I was getting a Pool Pilot but that was undertimed at the time of construction so I have a high/low timer that I will never use.

hmmm I am confused!

Diagram 1 clearly shows load out to pump so it would appear I should disregard diagram 1 as it is only for a one speed pump?

Let me see if this is what you mean:
I would attach legs 1 and 2 from the circuit to the line side of the timer.
The load side of the timer would then go to terminal connections 3 and 4 while still having the power jumpers between 1 to 3 and 2 to 4.

The output side of the Pool Pilot would stay the same out to Pump for a two speed configuration.

Correct?