Treatment options for rectal ulcers

I’m a 42-year old female. I’ve had Crohn’s for 10 years, and was diagnosed with UC for 10 years previous to that. I had my right colon removed in Feb 07. In Oct 07, I had a colonoscopy which revealed 2 rectal ulcers. I took a 7-day course of Flagyl, which caused diarrhea, and probably aggravated the situation. After that I took Cipro, and then started Remicade in Jan 08, and continued until Sept 08 when the Remicade stopped working. The Remicade had slowly reduced the size of the ulcers. I have been in excruciating pain from BMs (4-6 per day, mushy consistency). Sometime the pain would linger all day, making it difficult to walk and sit. My GI doctor’s next recommendation for treatment is Humira. I’m reluctant to switch to this. I would like something that more directly targets the ulcers, not a long-term treatment for Crohn’s overall, because I’m not having flares.
Two weeks ago, I developed a Bartholin gland infection, and was prescribed Augmentin. In addition to healing that infection, this seems to have improved my ulcers. The extreme pain I used to feel is now 20-30 percent of what it used to be. The Augmentin was a 10-day course, and I fear the unbearable pain will return now. My GI does not want to prescribe Augmentin long-term, because of increased likelihood of C Diff. I’ve read about this bacteria, but I’m wondering if the Augmentin has tackled other bacteria contributing to the ulcers. I would appreciate any suggestions about the effectiveness of Augmentin for Crohn’s or ulcers, or other suggestions for treatment.
Thank you. -- lynn024

Thanks for the reply, Nanners. I take Solaray Acidopholus, which has 3 types of probiotics. Anyone else with rectal ulcers who can share their experience? Thanks -- lynn024

Interesting ... my doctor hasn't mentioned any topical treatments at all. Maybe my condition is too serious for that? -- lynn024