I have lots of questions!

Fertility wise, the quick answer is no a jpouch will not affect it, nor will flagyl.  A few men do have dysfunction after the op but it usually improves.  Any issues are usually physical (getting an erection) rather than damage to the swimmers themselves.

Regarding the first part of your query is hard to say without a diagnosis.  You say endoscopy and stomach, that is the other end of the digestive tract, and not something we on this forum would have much experience with.  Did you mean endoscopy or pouchoscopy?  Did you mean stomach or were your trying to politely refer to the bowel?  Probiotics are for the bowel, and won't help with stomach issues, companies spend a lot of money developing the products so they transport to the bowel without being affected by the stomach.

If you can clarify a bit in sure someone will be able to provide some advice

It must be really frustrating and tiring for you both to be losing sleep at night. I guess that's not uncommon at the beginning for us pouchers but I would have expected it to settle down by now. It sounds like there's definitely a problem, so perhaps it's worth pushing for a second opinion on getting the right medication to help with it?

As for sex - I was warned erectile dysfunction might be a problem when I had the op (I was 18 at the time) but it's never been an issue, nor has sex drive. I don't have kids yet, so I can't speak for my fertility levels!

This sounds like pouchitis to me. If it always comes back after a course of antibiotics then it's what's called antibiotic-dependent pouchitis. The most common treatment for that is continuous antibiotic therapy, ideally rotating between several different antibiotics at 2-3 week intervals. If his doctor is too inexperienced to manage this without losing his nerve (or reading more about it), you may need to find a better gastroenterologist.

I'm on Flagyl all the time, but I f I were getting hand or foot numbness from it I'd stop it forever. I don't know what "joint numbness" means, though. There are plenty of other antibiotic choices available, and a knowledgeable gastroenterologist would know about them.

Some people treat this with biologic medications instead of antibiotics, and that can also work well.

Good luck!

Thanks for your replies! I have a few updates. My husband decided about 2 weeks ago to go on a vegan diet. Weird, I know...considering his condition. My friend actually has the same surgery and when I told her she thought he was insane and said a plant based diet would really screw her up and she'd end up in the hospital! I myself was a vegetarian for a long time. I've wanted to switch it a vegan diet but it's often hard, especially cooking for two. However after doing some research and watching "what the health" my husband threw away all of our meat and dairy. I said I would do my best to find recipes that I thought would be OK on his stomach. Flash forward to two weeks later, his nightly issues are completely gone. Now, I don't know if this is necessarily the "plants" at work...but I think it's a mixture of both. He would often eat very unhealthy late at night and I think that contributed to some issues he was having. But, his joint pain is gone, and his stomch pain is gone, and he wakes up maybe once to use the bathroom during the night, as opposed to 4 or 5 times. I'm not trying to advocate as I know many jpouchers would probably get sick - but so far, this diet seems to be working for him! I think I've read on here (or another message board site) some vegan jpouchers, so I'm trying to do my research and figuring out what meals/veggies work best. I've been doing a lot of savory oats/veggies..rice/veggies. Also some lentils and beans. So far, so good...here's to hoping it stays this way! 

Greek yogurt with LIVE cultures is sooo much better for the gut and intestines to balance things n help the body do what it needs to. eliminating sugar will also help hugely as that is what will feed candida, yeast  and other bacteria.

flagyl can have some long term negative effects and destroys the bodies Natural ability to make healthy gut cultures.  myself, I'm highly allergic to flagyl .  might be good to see a colon/rectal doc to determine if its the stomach or the colon; I've found CR docs to be much more helpful than gi docs.

I was always told by medical friends that the fad for live cultured yoghurts, and yoghurt drinks like Actimel and Yakult, are complete placebos, as the bacteria don't make it past the stomach acids anyway?

The bacterial strains in most yogurt and other cultured foods/drinks do have a very low survival rate in the stomach. The strains in reputable probiotic products are selected to have much higher survival rate, and have shown real effects in decent clinical studies.