With the information that you gave above I come up with this.
1. You got an error 1 message which indicates a bad WATER TEMPERATURE sensor.
2. You installed the sensor and you got the same message
3. To test it you removed the sensor and got an error 3 instead.
This is what identifies the problem.
The sensor that you swapped must have been the FREEZE TEMPERATURE sensor and not the WATER TEMPERATURE sensor.
The error 3 code only comes on when the FREEZE sensor is diabled or disconnected.
Solution: Trace the TEMPERATURE sensor and replace this sensor. The original freeze sensor is probably still good if you still have it.
Check out this manual and refer to page 38 "problem solving"
http://www.pentairpool.com/pdfs/cp3600OM.pdf
Refer to page 18 for the low voltage wiring diagram to find and trace the water sensor
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