I don't know how long I had c-diff before it was diagnosed. My GI took a stool sample during a pouchoscopy so it was treated before pouchitis. I was treated with flagyl and had to take it around 4 times before I was sure it was gone. I didn't retest each time as I hadn't been off of antibiotics for 2 weeks.
I believe most doctors would treat j-pouchers for pouchitis before testing for c-diff. C-diff isn't very common. I had c-diff several times when I had my colon and once it was caused by cipro. Cipro is prescribed for pouchitis and I won't take it as I don't want to bring on another case of c-diff.
I feel bad for you as it's nasty. I doubt you've had it all the time since August. I honestly don't know how I could have known to even complain to my surgeon about it as getting use to a j-pouch involves so many trips to the restroom and pain. I couldn't tell I had c-diff when I had my colon as it resembled flaring with UC. They all involve diarrhea.
I think it's a good thing you are on vanco. I never was and it took me a lot longer than 3 days to feel better. I hope you are feeling better ASAP. I'd never want to go through the first 4 months after my take down again - and compounding it with c-diff is just awful.
I still take s.boulardii probiotics as it specifically fights c-diff. You might want to look into this after you get off of the antibiotics.