Oh Poopsy, I'm so sorry you've had to go through all that. You need to get yourself to a great GI who will treat the Crohn's as aggressively as it's been treating you. There are some awfully good meds out there that can help you.
As far as Cobra goes, there is an extension if you become disabled during the normal time of coverage. Speak to your Benefits co-ordinator about it. You should also consider filing for SSDI if you have not already.
There is a type of auto-immune arthritis that often goes hand-in-hand with Crohn's. Spondyloarthropathy(SpA) or Spondylitis. It is treated similarly to RA and luckily, most of those treatments are the same ones used for Crohn's. Those of us with this type of arthritis kill two birds with one injection/infusion. Here's a link for more info about SpA. I seriously recommend that you have a complete exam by a Rheumatologist experienced in treating SpA.
It also sounds like you need to find a good Pain Mgmt Doc. The problems you are going through certainly are painful and you should have pain relief from someone trained in that area. Honestly, my Pain Doc, Rheumy and Endocrinologist are my 3 favorite Docs. I honestly don't know how I'd get by without them. If you noticed that I left GI off the list that's cause I want to smack him and am currently searching for a new one.
I sure hope that your Doc gets it together and finds some relief for you. If things keep on like this, get another opinion.