You have asked several questions in this note and I will try to answer them. Nasal washes are not a specific therapy, such as an antibiotic or antihistamine. They simply loosen the mucus that is in your nose and possibly the maxillary sinus to allow for better clearance and drainage. Doing this three times a day, if it is not a difficult thing for you, is not too much. All you are putting into your nose is a saline solution that is very safe. If the congestion and drainage improves, you can discontinue this treatment at any time and start again as it is needed.
It is not clear as to the cause of the pain you have described. It could be from your lungs, the lining of your lungs or in the muscles and nerves outside of the lungs. If this is a problem for you, it is best to see your physician to determine the precise nature of this and help to treat it. It is not likely that this pain has any direct relationship to the saline nasal washes. It is also not likely this is from mucus in your lungs. This would more likely cause you to cough, which you do not seem to have.
I hope this helps.