Based on what I have heard I expect the change to Shoemaker to be a significant change in protocol. I am used to taking antibiotics like Chiclets but I believe Shoemaker is a short-course antibiotic therapy doctor. If that is true for him than I am sure I am done with my antibiotics while under his care. That is certainly one thing to be very thankful for. I think his focus is on removing the toxins, lyme, etc., from your body.
To be fair I had been taking antibiotics and not seeing any improvement. I saw an initial significant improvement and then it just stopped. I continued with the antibiotics for a while hoping it would put me over the edge, but it never did. I quit all treatment because it was not helping. I hope this change makes some needed additional progress.
As it notes on his website he uses cholestyramine (CSM) to help remove the toxins from your body. I have taken CSM before and felt better while taking it. I stopped the CSM for a number of reasons. First, I was prescribed CSM to improve my contrast resolution, but I never saw a noticeable improvement. 😉 Secondly, CSM is somewhat vile to take. Lastly, I grew tired of having to coordinate taking it at an odd time safely distant from my antiepileptics. As a bonus the CSM constipation went away. I think you may need to live on prunes while taking CSM,