Tracy I'm sorry to hear all you've gone through today.
I can only tell you what I'd personally do. I'd want to know first if the samples they got today showed anything. The IM vet is right, endoscopic samples of the intestines aren't the best so if she got stomach samples today, there may not be a lot of benefit tomorrow in getting an intestinal sample. She thought his stomach looked abnormal, too, so you may get some answers there.
My choice for getting biopsies of the GI tract is laprascopic surgery. That's what I had done for my dog when he had liver issues, and that's what I should have done for my late cat Earl (more on that in a sec). It's minimally invasive and there is no extended hospital stay. They make three tiny holes in the abdomen (to stick the camera, the laprascope, and a tube with air to inflate the belly) and an experienced doctor makes the whole procedure go quite quickly. They can get good diagnostic samples of everything AND they can actually look at all the organs so that if, for example, your dog has a few weird spots on his liver, they can biopsy those exact spots. They can also do cultures to check for bacterial growth if infection is suspected.
Now about Earl. As some people here already know, I was given the option of trying endoscopic biopsies or exploratory surgery with Earl to see if his IBD had morphed into cancer. For various reasons I won't go into, it was almost certain that it had become a specific type of cancer. The endoscopic biopsies wouldn't be high-quality so I ditched the idea as not worth the risk, given the fact that this would be to confirm our suspicion rather than anything else and we were looking for intestinal disease and the intestines sample poorly. (Earl was a sickly cat at the time.) The other option, exploratory, I didn't think was worth it because the health risk of a full exploratory was high for a cat of his frailty. So we treated him presumptively, for the cancer we thought he had. When he died later, they did a necropsy (autopsy) and we were wrong, he had a different type of cancer and had been getting an ineffective chemo. His abdominal lymph nodes and his lower intestine were actually rotten with cancer, and it had spread everywhere. I had made a bad call which cost him dearly.
Since then, I have become much more pro-biopsy. Not just for treatment options, but for palliation options and prognosis. If I had known Earl had this type of cancer, I would have made different decisions which would likely have spared him some of the suffering he had at the end. At the time, our hospital wasn't doing laprascopic surgery and for reasons I can't fathom, his internist and onco didn't mention it to me because I would definitely strongly considered it, at least. Anyway, now I tell everyone about laprascopic surgery and I tell them the benefit of biopsy when a diagnosis can alter treatment and palliation decisions. Since Boomer is losing weight and something is amiss, you need to know where to go from here. The stomach tissue may tell you this; if not you'll still need some more information. Boomer is a young cat and could have years ahead, depending on diagnosis and treatment.
One last thing about ultrasound. I think ultrasound is a great tool and can give a lot of valuable information. It is also no substitute for biopsy or an actual eyeball-look, so in many cases I don't hang my hat on it. It gives a portion of information, it rarely cements a diagnosis. (Ok, once at my hospital the internist was able to see the rubber ducky a Golden Retriever had swallowed, sitting in the stomach, so that was a for-sure diagnosis, but it's unusual!) Earl's last ultrasound before his death was actually a "good" one -- the internist reported much less inflammation, smaller lymph nodes, etc. We learned with his necropsy that this was because there was really no healthy tissue left to be inflamed and his lymph nodes were falling apart. So the 'take as part of the big picture' caveat always applies for me.
