Your problems sound almost exactly like mine - I have been struggling off and on with a flare since last November (brought on by heavy antibiotic usage).
For the past month, I've pretty much settled into 2-4 BMs a day, and like you, about every other one will have a little bit of blood/mucous that is noticeable, primarily when I wipe (sorry to be graphic but I'm sure this is normal talk for all of us here!).
I am still taking 9 colozal a day, which I am hopeful has made the inflammation subside throughout the rest of the colon, but I do understand that lower region is the hardest place to treat. I have been doing the Rowasa enemas every third night (that is what my doc prescribed). I can't say I've noticed a huge difference, if anything, it almost seems the blood is more prevalent the day after doing the enema?
Either way, I also take Align, fish oil, and about a month ago started taking Metimucil - which actually has done a really good job of firming up my stools. If it weren't for the occasional blood/mucous, I would feel like things were pretty normal right now (I think I have IBS as well with a high stress job so I just know that naturally I go more than what would be considered normal).
At the end of the day, i've only been using the Rowasa since mid December, so I'm around 3 months - little longer than you, but again, have not been using it anymore than twice a week.
Dumb question - but am I correct with the thought that blood most noticeable from wiping is an indication of the blood being generated in the lowest part of the colon/rectum?