intermitten noise near front end area

I have a clunking noise when I start the engine sometime, I thought it might be the cooling fan or water pump, I have replaced cooling fan, water pump, serpentine belt and the thermostat. I the clunking noise stops once the engine is running, however, I have a clicking noise when car is in drive gear, sometime loud, sometime low, but much louder when I am in reverse gear. I checked the fluid level in the differential, its old but at a proper level. My next step would be to place the car on jack stands and check the universals and drive shaft while in gear. (Do you have any suggestions)