Thank you for the additional information.
If the medication has not made any difference then I agree that this is unlikely to be caused by allergies.
Dysphagia or difficulty swallowing can be caused by numerous problems.
Read more about all possibilities here.
One thing that I would discuss with your vet is a condition called Myastheia Gravis.
This is a condition that effects many large dogs and the first symptoms are difficulty swallowing and regurgitating food. This progresses to weakness in the facial muscles and or limbs. The trouble swallowing and regurgitating food is cause by the development of a mega esophagus.
Here is more on this problem.
Here is more on mega esophagus
Dental problems can also cause infection leading to a sore throat.
At this point the next step is going to be some additional testing. X rays of the throat will show any mega esophagus.If x rays shows that there is nothing wrong they may want to go down the throat with a scope to look for any growths or other problems. I would also have the teeth checked. Until you can have him seen I would try elevating the food/water bowl so he does not have to lower the neck and see if this helps.
I hope this has given you some additional options to discuss with your vet.
Edited by Candy on 1/23/2011 at 9:22 PM EST