I have a 2003 Comfortmaker furnace. When the furnace lights it starts making a clicking noise - then the burner goes out - then this repeats, furnace lights, makes a click then burner goes out. Could this be the thermo coupling? I pulled out the thermo coupling and sanded it a little with sandpaper but that didn't seem to work, Any suggestions would be greatly appreciated.

That is not a thermocouple but a sensor used by the circuit board to detect flame. The way you explained your problem I would have told you to clean that flame sensor well. Without the proper test equipment you are working under a handicap since you cannot take necessary measurements to find the defective part. I suggest cleaning that sensor again and if that does not work call for professional on site service to get it fixed before the real cold weather hits.