I don't see how your symptoms could be related. It's normal to try and find a link between everything, but it's not very logical that everything you are experiencing is because of one terrible illness ... especially when you have been checked out by a number of doctors and told that you are OK
What's more likely is that you have a few smaller, unrelated medical problems. If the cough got better with antiacid meds (which you said it did), then it was probably acid reflux! Otherwise, your cough would not have gotten better at all, right? :P
My BF gets acid reflux sometimes, and it's not always after acidy foods. Sometimes all it takes is a packet of TimTams (Australian chocolate biscuits)! lol Also, I don't mean to discount your symptoms, because I don't know exactly what they are like, but almost everyone I know gets a vague sporadic cough sometimes
As for the bumps, chances are that they are more swollen lymph nodes ... I can always finds bumps when I go looking for them. My BF tells me that rubbing them just makes them worse! I don't know if he's right or not lol, but the more I go looking for them the worse they seem.
Also, I know that anxiety can make eczema worse, so ... maybe if there's something that's linking all your symptoms together THAT's what it is. Considering all your other tests have come back fine, I would bet money on it, actually! lol
Try to relax and take a few deep breaths. I'm not a doctor, but I think you will be OK xx