Were you able to accomplish this. That is closing both adobe and pdf file using java script. If so, could you please let me know? We have exact same requirements as yours.
After a lot of research and tests, I didn't find the solution. You can't close Acrobat Reader from a pdf. (for security reasons; It's like you are not allowed to closed a browser with a javascript function).
Finally we moved to the PDF library C++ SDK, so Reader is no more opening, but we had to pay for that...
Thank you very much for your prompt reply. That will help me to decide what route to take. We are planning to use adobe livecycle java APIs and will print PDF directly to the default printer (silent print) without opening Adobe Reader.