I was just wondering yesterday how you were getting on. I did the full five days on my first pulse and felt nothing apart from undue tiredness and the ability to burst into tears at the drop of hat. Since I already had that to a lesser extent with he MS, I didn't think overmuch about it. The second pulse the same, except I felt somewhat dissociated from what was going on around me. No difference there, some would say. The real crunch came with the fifth pulse, when I had such intense thalamic pain moving around anywhere from my right shoulder to my right fingers. I temporarily lost much of the use I had regained in my right hand and arm because it was so damned painful. It would fade away, then come back in a different part of the arm. Next pulse, next to nothing, and nothing very much after that.
You have a nice way of describing the theory, but yes, flagyl can only kill something in the right stage of its development, otherwise you would only need one big go and that would be it. Have a look at this page, if you haven't seen it already:
Therefore it is not unusual for pulses to vary from one to the next. Come October, I would suggest that you time the flagyl pulse to come just after the scan for this reason. Hopefully your MRI won't be worse, but you might find it not much different. You want to aim at first for no worsening, then see what happens after that. New lesions might just fade away, if you have had something for a long while, but causing no symptoms, they might never go completely. Katman, LifeontheIce and I all know about this.
Please let us know how your next pulse goes!