I have PTSD and an autoimmune neurologic disease. I developed the autoimmune disease after getting PTSD. I agree with your therapist that getting a good medical workup is a good idea for many people with PTSD. Many diseases can make PTSD symptoms worse, and the on-going stress of PTSD can sometimes cause the body to break down a bit. Autoimmune issues are not the only thing. Seeing a good PCP who can work things up both in terms of sexually transmitted diseases, endocrine problems, neurologic issues, and autoimmune conditions is a good idea. Your therapist sounds smart and thorough.
That being said, it can also be very stressful to get a medical work up done, especially when trying to get the process started, and when waiting for results. I had to be tested for sexual transmitted diseases after an assault, and it was very hard to go in and talk about it, and especially hard to wait.
As hard as this is, try to take it one step at a time. The good thing is that you are dealing with it now, and in general, *if* something is going on, the sooner you find out, the better the outcomes generally are. Also, it could very likely turn out that you don't have anything going on, except PTSD - which is a lot on it's own! By getting testing and a work-up done, you will gain peace of mind.
When I have to go in for follow ups, to find out if the autoimmune disease is better or worse, I tell myself I'm going so that I can walk out reassured. I figure if the news is bad, there's no reason to get stressed before I know it is bad, when I can't do anything about it. That being said, I still have panic before almost every doctor appointment.
None of this is fair. I was just telling my therapist the other day that all of this sucks. It just does! I felt like a whiney little kid, ready to stomp my foot and yell at the universe for the hand I have been dealt.
No matter what, you have survived really difficult stuff before. You have to be made of strong stuff to get through trauma, and PTSD. Keep up the good fight to heal.