Since you have been two years on the PPI's with no relief in your breathing - perhaps your breathing problems are not related to Reflux/GERD. Perhaps they could be a side effect of the thyroid condition that you are being treated for.
Or, perhaps a side effect to one of the medications that you are taking. Medication Side effects do not always show up right away and can develop over time. Perhaps if you could convince your Dr. to switch up your meds just to see if that helps. I know at this point you must be getting quite desperate with your breathing problems :(
Perhaps the Lotrel is effecting your potassium levels negatively - also synthroid reacts with certain over the counter anti-acids so you may want to check with your Dr. before taking Gaviscon.
I really hope you are able to find some relief - some how, some way.