Hi Spartan,
Wow. when I read your post here I could really relate. And I really feel for you. I started the program in August and there were entire weeks in Sept. and October that I couldn't stop emoting - crying, upset, invaded (to use your word) by my thoughts. I do'nt recall reading any warning on this site about that happening but then it might be discussed somewhere that I didn't read since I jumped around when i went through reading all the toolbox items.
My reply to you is simply to stay with yourself as much as possible which is not to say, let the thoughts pull you down.
I have come to realize that deciding to address my anxiety brought me to my edge, or got me in touch with the depth of my anxiety to put it another way. It was not comfortable. It was not easy. It was not easy for anyone around me to understand what I had unearthed. It seemed like there was a lot of panic, and some days, nothing but intrusive thoughts.
My message is that this phase does not last forever. It is a phase. It was an important part of my progress. Davit and others here have lots of wisdom about how to balance your day to day so you are not overwhelmed by your thoughts. i am thinking specifically about the advice around coping skills and stress management techniques - knowing what makes you feel good and doing some of that each day to balance out with the discomfort that the invasive thoughts are causing.
My view of this program is that it gets you in touch with your thoughts and then one of the first things that might happen is that you might realize how many distressing thoughts you actually have and THAT can end up being distressing (to realize how deep the anxiety is rooted). Like I say, about 2 months for me were spent feeling around for this - with little to no support outside of this website. And I got through it. I am in touch with my thoughts now as a habit. and I know what to do with the distressing ones. But they ran the show for quite some time to put it mildly.
Hang in there and post often. I dont know all the answers of course but I can tell you that you are not alone in what you are experiencing. I remember others going through this when I was and the cured folks here were very good at reminding everyone tht taking a break (using meds or not) is not giving up on yourself. Its just taking a break. Which we might need. And that is perfectly OK.
The breathing exercises helped a lot and I was slow to commit to doing them. Do they help you? I also googled "breathing" to learn more about proper deep breathing techniques which helped a lot.