I know how frusterating this is...I can't stand to listen to my daughter cough and cough all night. With her she was always having these symptoms without being really "sick" like you describe, no fever, no runny stools acting normally etc...ever since she was 3 or 4 months old. So stuffy all the time and coughed alot. Could definately tell the difference when she had a true cold or was sick for real so this was very aggrivating for us as well.
Fast forward to about 20 months and we finally figured out it has been allergies this whole time! Although I must say that when she wasn't fighting allergies, she had alot of coughing when she was teething due to increase in saliva.
She was put on Zyrtec (tried claritin, didn't work well) but you need to realize that it may take a while so keep at it until it gets built up in her system. The first time we gave it to her, it took a good 2 1/2 weeks and then VOILA! she stopped coughing. WE could all sleep. But as she got older (she is now 3 1/2) we had to add a chewable by mouth and the zyrtec and occasionally a nose spray when she is really bad. If we stay on top of it, she is symptom free or at least 80% better.
Good luck