I don't think any of your theories explain the enlarged kidneys.  Did the vet rule out lymphoma? That can occur in the kidneys and intestines, is common in FeLV+ cats, and responds well to dexamethasone (it shrinks lymphoma).  It might not have anything to do with lymphoma, and I hope it does, but if it does chemo might help in addition to dex. What were his kidney values like on his blood panel?
Michelle

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