Thanks for writing and for doing this work and for being so brave!
You are absolutely correct that those issues that they are "seeing" on your MRIs could not cause widespread symptoms such as you have. So, you really need to banish those worries from your mind. Sometimes, this advice (when followed) makes all the difference in the world because you can then really relax knowing for 100% that there is absolutely nothing wrong!!
That being said, it is very common for the brain to create flares and ups and downs. It's just what it does and it can seem very random and be very discouraging. However, the most important thing you can do is to not worry or get discouraged even if you get episodes of severe pain. That doesn't change the issue, which is still this: It's your brain doing this and nothing more; you're going to be fine; but you can't worry about it and you can't fret when things get worse for a while.
Does that help?