Just wanted to correct something. The large intestine does not just absorb water. It houses most of the gut flora which are responsible for so many functions that we don't know them all yet, such as neurotransmitter production. Also, ileostomy often reduces the ability of the small bowel to absorb nutrients like iron and B12, so it's not like the small intestine has perfect absorption after an ileostomy.
I support the choice for surgery but it's good to be comprehensive when people really want to understand what they might be dealing with.
Flaring for years and years sounds terrible. I hope you find relief soon, no matter what you end up choosing