I would not be at all surprised if this was a primary upper GI problem, and not related to your pouch, per se. Sometimes surgery can trigger other issues, such as dyspepsia, gallbladder problems, etc. It can seem that antibiotics are causing the problem, when it is very possible that they are only revealing something that was already there (by altering the gut flora). Gas is an extremely common symptom, and I just don't think you can relate it to just the rectal cuff. But, if your cuff is inflamed, it will react with pain and/or spasm to pretty much anything that is irritating, and gas is definitely irritating to the gut. It is not irritating in the inflammatory sense, but in the sense that it causes distention and pain. Sometimes probiotics help with this, sometimes they make it worse, and it varies by the type and even the different strains of the same species.
So, about the only thing you can do is go back to baseline (Ensure), and only change one thing at a time. That way you can really know how each thing affects you. When you change different things simultaneously or even within a few days of each other, you cannot tell what is doing what. 20 days of antibiotic should have done something positive if it was going to.
As to liquid vs. solid stool, I am not sure liquid is so bad, as long as you are continent and reasonably comfortable. My stool tends to run mostly liquid most of the time, whether my diet is liquid or solid, and as long as I can delay bowel movements and do not have a high frequency, I do not worry about it.
I agree with you that increased gas is very problematic, but a short course of Flagyl ALWAYS takes care of it for me. I've never had Cipro, so can't comment on that. I've had other antibiotics for unrelated infections without incident, but we are all different.
Jan