I've had increasingly bad dysautonomia for about a decade, and just found out about 6 months ago that it's because I have peripheral neuropathy from Sjogren's (also autoimmune). Personally, I couldn't take Cymbalta or any antidepressants because they drop my BP like a rock, but I know it helps some people. I'm taking Plaquenil for the Sjogren's, the idea being to get my immune system to stop attacking my nervous system, so that maybe the nerves will start growing back eventually.
Peripheral neuropathy is VERY common with autoimmune diseases, though often not diagnosed or misdiagnosed as fibromyalgia. If you want some reading on Peripheral Neuropathy, this MedHelp page is decent. There's also quite a bit of info on the web, although most pages gloss over all the autonomic problems.
http://www.medhelp.org/medical-information/show/74
Right now, I'm waiting for a Lyrica rx to be approved by insurance and am in excruciating pain. I'm not very familiar with treatment for colitis or ankylosing spondylitis, but I will read up on them when I'm feeling a little better so we can converse a little better. I'll get back to you when I don't feel like death warmed over.