I agree with anmllover regarding the ET tube placement. Check with your vet to see if they used one with your dog. (Some don't on males) Another possiblility is he had a lowered iimmunity due to stress and the Sx and it caused him a cold.
Many Shepherds can have GI issues. First, a good quality diet is important, regular dewormings, and digestive flora are superb. A new one your vet may already have is by Purina (Althought I DO NOT recommend their foods) called FortiFlora. I am sure your new dog is causing stress. Help your GS by building confidenceand reestablish leadership/pack rank in your home. Try www.ddfl.org for behavioral assistance.
Hope this helps, D