When I connect the 240 volt motor directly to hte GFCI breaker it works fine, however when run throough the time clock, when I turn on the breaker, it trips the breaker

You have T104 timer that controls 240Volt motor.
You have 240Volt GFCI breaker.
GFCI to motor works fine.
GFCI to timer trips breaker.

Either timer is wired wrong, or ground fault in the timer.

Open following links to review wiring:
http://waterheatertimer.org/How-to-wire-T104-Intermatic-timer.html
http://waterheatertimer.org/images/T-104-control-240V-Load4-35.jpg

1) Make sure clock motor wires are on terminals 1 and 3, and that clock motor is 240Volt WG1573 and not 120V WG1570
2) Try connecting GFCI hot leads to terminals 1 and 3 and don't connect wires to motor.
3) Click manual override both directions and see if a short appears.
4) Remove ground wire from timer but leave power connected. Test metal timer body to ground wire to see if there is power flowing to ground.
5) Unscrew clock motor from body, and make sure clock is not touching metal body, repeat test to ground to see if clock motor is bad.
6) Remove small white wires that power the clock, to test if clock is shorting. Replace WG1573 if clock is bad.

7) Connect 240Volt motor to terminals 2 and 4. Click override back and forth. Then reverse wires to 4 and 2.