I have a clear jelly like substance in my stool. it will appear for a few days, then go away for 6 months or so, with cramping.

Intermittent mucus: Mucus discharge occurs in up to 50% of patients with irritable bowel syndrome, with or without pain. Mucus may also be produced in response to partial obstruction, chronic constipation, rectal dysfunction, infection, & even from secretory villous tumors of the rectum. At the very least stool studies & probably a sigmoidoscopy should be considered, but a more extensive evaluation may be warranted.