I have removed the wires connected to are and C. Then removed the batteries and waited 2 minutes. Then replaced the wire and replaced with new batteries. The furnace will kick on but eventually stops about 4 degrees less than the desired temp. Any suggestions?

For how long does the unit runs? Its it working properly or its just the fan running

About 5 minutes. The furnace is working fine. Definitely thermostat related

It's it a new Tstat or old? Did it just started doing that? Do you have the manual, if you do check to see if you can calibrate the temperature.