Philip, first I would like to say welcome and all messages here, like in SFQ, a form of energy. Thank you for sharing yours.
The second thing, is you are not supposed to used the word diagnose in SFQ. It's just a legal thing. Only licenced medical professionals diagnose. However, sharing your thoughts on what you think is your problem is wonderful. It all the more energy for us to experience.
The third thing is your second last paragraph is your best advice in a nutshell. Your currently experience is similar to the ones you alluded to having earlier. They seem like problems when they aren't progressing as we expect, but later on we can see they are just part of the process of healing.
That's where the Trust come in. You don't have to consciously understand what is happening to you during your own exercises. You can just release your worry to the universe and Trust it is part of your healing. The more experience you have in trusting and then seeing the healing occur the more confidence you will gain.
So I'll echo your own advice. Just chill. You can control your thoughts. If they stray, smile and bring them back to the meditations as directed. If you feel the energy someplace new. Thank it. Don't follow it or fight it. You need only do the meditations and experience however you and the universal energy are combining at this moment.
Remember you are not aware of everything that is happening, you can't be expected to understand it all. Just trust in the universe and someone with better vision than us.
I once ask Master Lin a similar question, but mine was about a very nice experience. His reply was short. He said you don't understand what is happening. I wasn't the smart*** and say Duh, that's why I asked you! I understood that it is my answer. I don't understand. I trust in the good of what I am doing. I am positive and I, with the universe, will create the positive.
Trust and stay positive.
You are perfection.
Iam2 
