(I only need for this thermostat to control my Amana A/C unit).

I did not record the old thermostat wiring before replacing with the new Honeywell CT-31 I have connected the R wire to R terminal; G to G Terminal; W to W terminal. This caused the thermostat to function partially but only when the thermostat switch was set to 'Heat'; the fan operates continuously regardless of temp setting - fan only powers off when switch is returned to 'off' position. Compressor seems to function properly but this is moot when using the Heat setting.

I then moved the W to the Y terminal and now the fan unit seems to be functioning fine with the thermostat set to 'Cool' - the temp setting seems to control the A/C unit properly. The problem is that the fan continuously runs until setting back to the 'off' position manually (the temp setting only controls the A/C unit properly and not the fan).

Do I need a jumper? Are the R,G wires on R, G terminal respectively, the problem?

Try moving the R wire to RC. The RC is for cooling the RH is for heating.

Since you already moved the other from w to Y it should work.

Post back with results.

A copy of your instructions below.

http://customer.honeywell.com/techlit/pdf/69-0000s/69-1809ES.pdf

There are only 4 terminals on the Honeywell CT31 tstat (R. W. G. Y.). There are not RC or RH terminals

Then you might try placing the G terminal with the wire on the y terminal. Do not jumper just put both wires under the y terminal.

If you just jump them anytime you move the blower switch from auto to on it will cause the ac to run without thermostat control.

By placing the g with the y whenever the thermostat calls for coolinhg it will also bring on the blower.

The thermostat should have internal workings to do this but why yours is not working I have no idea.

you can always call Honeywell on there toll free number.