lol I didn't mean a gut wrenching loud belch. If there is urease activity it would depend upon the quantity of bacteria and their urease capabilities. Some urease bacteria are very strong but others are less so. It's possible that the small burps you get could be due to the carbon dioxide produced by the neutralization of your stomach acid.
I think that it would be worth you trying the acid test to find out if there is any evidence of urease activity. It doesn't really cost anything, you can use what acid you have, even vinegar, lemon or AVC if you have some.
Taking some such acids as drinks with food might help your digestion a little bit as well.
It doesn't sound like you are digesting very well and finding out why would help you to make progress.
The following site explains reflux and why it occurs, insufficient stomach acid and a ph which is not low enough.
I don't know any reason why worms would prevent the stomach from healing. It could be a lack of nutrients required to heal or body processes which cannot get the required nutrients. Magnesium is crucial to so many processes and it's absorption is seriously affected when there is insufficient acid and digestive processes. Common forms of magnesium require oxidation in order to be absorbed. I became hypothyroid when I stopped taking mag malate and switched to mag oxide to save costs. Your thyroid problem could be down to lack of magnesium because of lack of stomach acid.
At least until you can get your stomach working well, I would get an absorbable magnesium to ensure that everything can work properly and not delay healing. Magnesium is such an important mineral which can affect so many enzyme systems and activating your thyroid hormones.