pancreatic enzymes with every meal, 1/4 tsp from memory.  And start B12 injections, 0.5ml weekly 6w then monthly thereafter.  Continue with low residue/hypo diet for presumed IBD.  See what effect this has and then add in metronidazole or prednisolone for IBD if diarrhea not fully controlled with enzymes alone.

A GI panel would rule in/out pancreatitis and EPI (fPL & TLI) If these were normal, I would then be discussing endoscopy or exploratory with the owners to confirm my suspicion of IBD and to characterize it so as to better treat it. Exploratory would be preferable because you would get a better biopsies of the intestines (full thickness) and would also be able to biopsy the liver and pancreas at the same time.  Endoscopy is less invasive, but more limited in its scope. If the owners were unable or unwilling to get biopsies, I would have to put the cat on prednisolone as an alternative. 

I would deworm anyway with Milbemax - false negatives are common with faecal flotations and I have to assume that she is exposed to internal parasites by virtue of her lifestyle.  Once now & repeated in 2-3 wks.   How much is the URI affecting her?  Is she appetent? Is she spayed?   Metronidazole (10mg/kg) certainly be a useful antibiotic to tamp down the anaerobes that may be present and producing gas, as well as a treatment for possible giardia.   The URI may be solely viral and, with better nutrition, deworming and a resolution of the diarrhea, may be self-limiting.  Depending on the severity, I may hold off on treating this specifically until the other issues had resolved. If it did affect her, I would consider Baytril (doxy is my first choice for URIs, but may cause too much GI upset).   Diet - wet chicken/rice variety, like i/d or gastro, little & often feeding schedule. Need to feed those villi to get them to heal, without asking too much of them!  I would additionally add in a probiotic to help adjust the bacteria in the gut (Fortiflora or similar).   How'd I do?