As I said, start flagyl only when you are taking the full dose of doxy et al and when you are getting no reactions from them. I started at about three months only because of this: you will regret it if you start differently. You might feel after the first pulse of flagyl that this is a breeze: I did, but you might feel differently with subsequent pulses.
You can take all the doxy in one go: I did after a few weeks because it makes life easier!
Best of luck!!
An Itinerary in Light and Shadow Completed Dr Charles Stratton / Dr David Wheldon abx regime for aggressive secondary progressive MS in June 2007, after four years. Still improving with no relapses since starting. Can't run but can paint all day.