MALT Lyphoma in an FAP patient with j-pouch pull thru

My story is a long one, I'll try to be brief. I am in my late 40's and have FAP, I've had a surgery years ago that took most of my colon and reconstructed my bowels with the part of the small intestine. I believe it was called something like J-pouch pull thru (or something to that manner). I also go every year for my upper and lower endoscopes. About four months before my last endoscope, I started to notice blood on the tp after wiping, and trace amounts of blood in my stool. It was also about this time I started to have pain in my epigastric region and to the upper right side by my rib cage. Sometimes the pain was so bad I would take pain meds to relieve it, and it took the edge off, and I was also going through such violent vomiting episodes which averaged once or twice a week, and felt nauseated constantly. I also have not had my period for over seven months. So I explained all this to my doctor doing the endoscopes, and he explained it away, I felt comfortable with his explanation, so when the procedure was done I went on my merry way... A week later I get a call telling me that two of the polyps found had trace of MALT lymphoma in them. Ok, so two weeks after that I saw the hematologist who told me I should be fine, he explained that the polyps were found on the part of my small intestine that was used to form my rectum, and that it is more likely related to h.pylori. I'm thinking alright, but what about the pain and the fact it can go from a 2 to a 5 in a matter of minutes with no relief other than pain meds. He reluctantly prescribes me a very low dose, and my nausea. He made me feel as though it was all in my head. I had a CT scan done which revealed two nodules on my thyroid, and something on my adrenal gland, I was told that this would be something to look at later down the road. Anyway, I was never tested for h.pylori, I did however have blood drawn, and my wbc was elevated, eosinophil and neutrophils were elevated, which I was told could be the lymphoma. LDH was 593, I was told I was fine and see you in four weeks for another blood test.
So now I've been off the prepack cocktail for about three weeks, I am nauseous all the time, I barely eat, I wake up every night in a pool of sweat, having to change my tee shirt and pillow cases because they're soaked. I am in alot of pain now it seems even my bones hurt. All I want to do is sleep. I'm praying this is still just the side effects of the antibiotic cocktail. My question is, should I be concerned about the results of the ct scans with regards to the thyroid and adrenal gland and seek a second opinion, or am I just being a hypochondriac?  (please excuse the spelling...)