Please, when you go to the vet, have your dog checked for the possibility that it has megaesophagus. The symptoms you describe are very similar as those for megaesophagus. It is not a common condition, so many vets don't know much about it. As a result, they often don't think to consider it as the reason for a dog choking after eating and during the night.

It's best to educate yourself first, and below are some places to read about it. You may have to educate your vet about it, too, unfortunately!

http://www.marvistavet.com/html/body_megaesophagus.html
This page has an animated description of megaesophagus

http://groups.yahoo.com/group/megaesophagus/
Read back through the messages here and check out the Files and Links. If you register, you can ask questions of the members who know alot about the condition.

http://www.geocities.com/bailey_chair/
This describes the Bailey Chair for dogs with megaesophagus, designed to help with their feeding.