How about
D) Leave it alone, or if you ant to change the filter, go ahead.
Lifter noises and similar things are common during ARX treatment. You will find many posts advising patience. I would not freak out and alter the course of treatment over this. Lifter noise for 3 minutes in the morning is neither too atypical nor alarming in the range of experiences in an ARX cycle.
1. Don't add the MMO to the autoRX rinse phase. It probably wouldn't do anything bad but also probably nothing good and it would be better just to leave alone and not interfere with the ARX chemistry.
2. If it makes you feel better to change the filter, go ahead. If you really want to change the oil mid way through a rinse cycle you could, although i don't think that is your problem and I think 100 miles in is pretty early.
I changed my oil 800 miles into an Auto RX rinse cycle because I had started with a 15w40 HDEO dino and ended up not driving as much as i expected. Since minus 15 degree temps are common here I wanted to put in a thinner oil. At about 800 miles into the rinse I asked the AutoRX guys and they said it would be fine. I changed oil to 5w30 dino and filter and drove the remaining miles, then drained and switched back to 0w40 synthetic.
I have found the AutoRX guys very helpful if you ask a question that shows that you have studied the directions and understand the basics and have a requirement not explicitly covered. eg "I thought I could get 1500 miles in before winter but I am really sketchy about leaving a 15w40 oil in during a canadian winter. Can I drain the rinse oil at the mid point and replace with 5w30 Dino?" will likely receive a more helpful reply than "I am the 100,000th person to notice some lifter noise during AutoRX application. Should I panic and dump some thinner into my oil or change it all out?"