Hi Bill;
I have the same thing. I was constantly choking and coughing when I first started "learning" how to eat and drink again. Now, six months out and it has gotten much better. A speech therapist helped me a lot with the problem as far as situating food and swallowing with restricted muscle control and a "smaller" throat. I also done the "clearing" thing all the time. She asked me to focus on eliminating that, or to concentrate on a full cough (like the Ahem xynobix references) when doing it, as opposed to just a small throat clear. I was informed that all of this has a "reflux" type effect and would further the irratation I was already experiencing. Once I was made aware of it I found it easier to control. Improvement has continued, and as my saliva has improved so has the lack of need to clear my throat so often. I still choke easily though, (especially when I forget and get a little to aggressive while eating) something that we all will probably continue to endure after treatment we were subjected to.

Steve