I've got to say, you're making me really nervous. Messing with pool wiring, if you don't know what you're doing, is a great way to hurt yourself, hurt your family, or destroy equipment.

I deleted 2 of the attachments; they were too small to be very useful. They did provide some info: you have an I-matic T104R timer, which I believe is an 24hr DPST timer. (T104R instructions) And you have a 3/4 HP Whisperflo. More info is needed.

Let me summarize what I think you've told us; please correct any errors:

1. You have a 3/4 HP Whisperflo, wired for 120V.
2. You've used extension cord cable, inside NMT flex conduit. This cable has only 2 wires, and no ground wire.
+ ? Is the extension cord cable coming from the power source (GFCI receptacle) or going to the pump?
+ ? Why are you connecting a pump to a GFCI?
+ ? Why is there no ground wire on one of the connections?
+ ? Why do you have flexible cable INSIDE conduit?
3. You're installing a metal case T104R timer, which MUST be grounded AND bonded.

+ ? Do you understand the difference between bonding and grounding?
4. A Whisperflo can be wired either 120V or 240V.
+ ? Are you sure your pump is wired 120V?
+ ? At 120V, all wiring must be 12 gauge, and must not be longer than 100ft total distance from a main power panel. Longer runs must be fed from an intermediate panel, wired with #10 or larger. Have you checked this?
+ ? Do you understand that undersized wiring can 'kill' your pump?
5. The T104R is intended for use with 220-240V circuits, but can be used with 120V circuits.
+ ? Do you understand the way US 120/240V house wiring is done, with L1, L2, C & Gnd, where L1 <-> L2 is 240V, L1 -> C is 120V, and L2 -> C is 120V and C <-> Gnd is 0V?
You're a subscriber, so I'm going the distance here with you, but I'm getting the feeling you're in over your head on this one. Please email LARGE pictures to poolforum@gmail.com, and include ALL of the following shots:
1. Pump motor label.
2. Over all shot that includes pump, timer, and power source for timer.
3. Shot of the power source for the timer (GFCI?)
4. Shot of the end of the 3 wire cord, and also of how that cord relates to the NMT flex conduit.
5. Shot of the end-bell of the pump, with the electrical cover plate removed, showing the way the pump is wired.
6. Shot of the pool (what kind of pool do you have?)


I can't emphasize enough: do this wrong, and the best outcome will be that you destroy your pump. But making mistakes with this could kill a family member -- I mean that literally, not figuratively, as in, "Call the morgue, not the ambulance!".