
Hi there,
This is a tricky one, and I'm not sure I'm the best person to respond, but since nobody else has had a go I might as well try! I have to say that it sounds like he had excellent care, so it may be that he's going to be one of those 'mystery cases' that never really gets solved. Given what you've mentioned I wonder if there are two issues at play here - the main underlying issue, and then the inappetence causing the fatty liver, enlarged pancreas etc.
My first thought is IBD. It's a tricky disease, and it's now thought that IBD and intestinal lymphoma are part of a spectrum of disease. The waxing-waning nature and disinterest in food, along with the weight loss, are suggestive to me - although the anemia doesn't fit unless he's extremely malnourished. How are his poops? Other things that bounce around my head right now include a persistent foreign body (not enough to be an emergency, just enough to make him nauseous), or something viral (lots of possible candidates).
My second thought is that you don't mention any imaging - ultrasound or x-ray, or something more advanced - unless I've missed it in the essay (lol!) so I would definitely be looking at imaging (ideally ultrasound) to get more of an idea what's happening with him. You've also mentioned bloodwork, but not specifically what was done - I would be checking FELV and FIV if they haven't already been checked.
Either way I would urge you to talk to your vet if he starts going downhill at all. It sounds like a referral to a hospital with an internal medicine specialist is the best option to get to the bottom of this. A university may be the best option!
Hopefully some of the other vets on here have some more ideas for you.
Please let us know how your little man is getting on!
Best Wishes,
Dr Woodnutt