Installing Honeywell WiFi Thermostat
I would remove the jumper from Y to G and use your yellow for Y. 

On the thermostat and the furnace you should have
Y , yellow (cooling)
G, green (fan)
R, red (power 24v) jumper R to Rc, Rh
W, white (heat) no jumper, on thermostat use W1 (first stage heat). Leave W2 unused and set the thermostat to single stage heat, single stage cool, that way the thermostat knows that there is nothing connected to its W2 terminal. 
C, blue (common/ground) this wire allows the thermostat to draw power from the HVAC system as opposed to using the batteries.