The first thing I would do is start floating your dog's food every meal. Add water to it every meal. Like... a lot of water. If she doesn't drink the water to get to the food and manages to just pick the food out of the water, add the water earlier and let the food soak up the water - it will turn all puffy and big. You need to increase her water consumption.
I would guess that's why Honest Kitchen works for people - having to rehydrate it means adding water and increasing water consumption in the dog's diet, and that's huge in helping fight off stones and crystals!
Then I would ask for Baytril instead of Clavamox. Clav is a cephalosporin, and Baytril is a fluoroquinolone, so they will attack the bacteria differently. If Clav isn't clearing it up and it's Enterococcus, time to try a fluoroquinolone instead.
No more blood makes me think you probably don't have bladder/kidney stones, but it's a possibility... your other option besides changing diet is to do an x-ray and if there are stones do bladder surgery to remove them, then send off the stones to be analyzed so you know exactly what you're dealing with and how to combat it in the future.
Struvite crystals, and stones, can be dissolved with diet. You'll be looking for something low in protein, low in magnesium and calcium, and low fat. Technically you're looking for something low in a particular type of protein, but I can't recall exactly what the deal is. I know there aren't many commercial foods that fit the bill outside of the crappy Rx diets. =/
So, yeah. First add water to her food. Get her to drink more. You can purchase low sodium chicken broth and add a little to her water dish too, get her to drink more that way. Make sure she has plenty of opportunity to go out and pee throughout the day, too. Then try the Baytril. Hopefully that will resolve the problem for now and in the future.
There are a few holistic blends you can add to her meals to help prevent it in the future too. Cranberry is a good one, this is the one I use for Auggie:
Tinkle Tonic
My holistic vet recommended it to me and I was pretty much desperate to do anything to keep Auggie from getting bladder stones again, so I bought it. We've been free and clear since his bladder surgery, though I do have a urinalysis run every two to three months now to make sure we're still all good. Several of these ingredients are mentioned in Dr. Pitcairn's Natural Health book as being good for bladder health so I know it's not random mumbo-jumbo (unless you think all holistic medicine is random mumbo-jumbo haha.)
ETA: Just saw your post about the x-ray, so disregard all that. I would switch to the Baytril. Enterococcus can be resistant to one or even both types of typical antibiotics. If the Baytril doesn't work you'll need to explore a different route. I don't remember the name of the stuff that has to be used if it's resistant to both antibiotics. It's given as an IV IIRC.