Has the Flagyl provided any obvious benefit? Your story sounds like not. If not, you've been on it way too long, IMO, and should probably try a different antibiotic, like Cipro. I'm guessing you have pouchitis, and (if I've got the story right) it's never been treated successfully. Cipro might give you very quick relief. If it does, then you probably don't need the Cortifoam, either.

This isn't a giant mystery, in all likelihood. It's common for any particular antibiotic (e.g. Flagyl) to not work, and a different one just needs to be tried. When my pouchitis first developed Flagyl was ineffective. I was lucky enough that my GI simply switched me to Cipro after perhaps ten days, and it worked like magic. Good luck!

I've found my gut bacteria to very fussy. I'm now almost 7 years post take-down and I try to avoid antibiotics. At first they really help, but after a week things start to slide. I actually just finished a round of penecillin for strep, 7 day course and my pouch is a mess now. I've made and effort over the years to build up gut bacteria and I think rotating and timing probiotics and pre-biotics is great. Right now I take florastor, 1 immodium with meals,  and then psyllium husk after. Organic india is the best, way better than anything for me. It's so personal but I think it's good to experiment. Probiotic foods are great, yogurt, pickles, kombucha. You might need more immodium at night, and it builds up so you have to find a balance. I've over done it and gotten a blockage before and that hospital trip is not fun. When and what I eat and how I combine foods seem to have an impact. Mixing veggies, beans, a starch and protein really seems to bulk me up. Any of those alone and I'm loose.  It really does sound like the antibiotic could be creating a void in there and working against you unless pouchitis is the official issue. Per Scott you may very well need a different antibiotic but maybe a rest in between could help! Of course listen to your GI. For me at least, without the right balance in there my pouch always feels a little achy and weak, like right now -- post antibiotics. It will just take time to build back the right balance for me. I think it's easy to measure these things on a day to day, when the progress is actually seen more week to week or even month to month, and two years in was so different than 6 moths for me. Much more stable. As for the blood it could possibly be coming from the tiny little bit of colon your surgeon used to stitch your rectum to your pouch. Just a guess... I get that from time to time.

I guess my take-away would be that antibiotics play a major role and are sometimes needed, for some more than others but it's equally if not more important to get the routine with food and probiotics, fiber, etc right for you and that takes some serious tweaking and experimentation. We all have trigger foods. Popcorn or sausage will land me in the hospital with a blockage in a heartbeat. Maybe keep a journal and food diary so as not to introduce to many things at once? With too many frequent changes you can get lost in the woods ya know. 

There are ups and downs but it's certainly better than UC!

 I take 1 loperomide morning and evening and half a tea spoon of psyllium husk.  The husk does add bulk but i find I have to drink a lot more or get quite severe cramping.  Without it I get more cramping but it's less intense.  Perhaps try removing the fibre for a day or two and see what happens?

Also do you need to take loperomide and lomotil?  Could you get away with reducing the dose as that would affect your guy twitch.   I'd try the fibre first, see what happens though

I would personally never take both. I do occasionally switch between lomotil and immodium from time to time as I feel my body builds resistance and each becomes less effective. I usually take Imodium because it's cheap and requires no prescription and my health care plan sucks.

Dehydration could also be playing a factor... Are you drinking enough water??? I have to drink twice as much water as I did pre pouch, maybe more, and the ballance of Imodium and fiber helps me stay hydrated. I also drink a sugar free elctrolyte powder called Ultimata. Dehydration is a slippery slope and can masquerade as other symptoms, loose stool, cramping etc. Once I get a little dehydrated it can be a runaway train and the above symptoms can escalate in my experience. I've had hospital visits and needed IV liquids before. It also sets off my eczema, joint pain etc. I highly recommend yoga/meditation and anything that helps you feel your body and organs included, general exercise is good. Living in your physical body. We've experienced so much physical pain it's easy to try to shut that side out, and compartmentalizing pain can be usedul but ignoring the body, for me at least has led to problems. That's a mouthful, but overall adjusting to that "new normal" is a major life change and there are always new issues that arise so be vigilant. I try to think of my pouch as a gift even when it gets cranky. Any day without my damn colon is a good day.

keep experimenting in little ways till you get the mix right!

I just thought of this but could you have an adhesion??? I suspect I may one actually. Maybe some folks with more pouchitis experience can chime in, I've had it maybe once or twice if at all. 2 months seems like a long time on Flagyl with no relief. Also 6 Imodium/day and 2 lomotil seems like an aweful lot to me. Per above I don't think many folks mix them and more than 3 immodium per day and I'm in trouble. Slightly oatmeal like stool is normal for us, it's not reasonable to expect fully formed like with a colon. Too much immodium for me causes rebounds and stress on my guts, formed stool and cramping as it moves through me then a rebound with liquid stools and high output.

I hope you feel better soon!!!

My son had a setback about 18 months out.  Flareup, new Crohn's diagnosis.  Seemed to calm down with Pentasa, which he's still on another year and a half later.  He also takes Omega 3 and probiotics: Deva Organic Vegan Vitamins Flax Seed Oil, Omega-3, and Nutrition Now PB 8 ProBiotic Acidophilus Vegetarian.  He eats pretty much what he wants, keeping down on spices (like too much pepperoni pizza).  Pentasa is very expensive without good insurance, but it can be had from Canada at about 1/5 the price.