Here are some replies to your questions:
Long term treatment with these antibiotics essentially causes no problems, since they are carefully chosen to avoid any problems with resistance. Doxycycline can be taken long term without difficulty and often is for, say acne, and can then be used eventually intermittently with no problems whatsoever. Many people use this as a prophylactic against malaria.
Consequently if you need to take doxycycline for any reason in the future, no worry. The regime also does not affect any other antibiotic you might need to take at any time in the future. While you are taking them, there are many illnesses that you should not be bothered with in any case.
You can certainly both eat and drink normally during the treatment. The only thing you should be careful about is drinking during the five days you are on metronidizole. Also, it is advisable to take probiotics, such as acidophilus during the course, at least two hours separate from any of the antibiotics. This should avoid any intestinal problems.
Bear in mind that the person who started me on this treatment, my husband David, is a consultant microbiologist, and so knows exactly what one can and can't do with the various antibiotics and would not want to cause problems either to me or to anyone else in the future. A fellow microbiologist at the time said, 'but aren't you worried about thrush?' - an easily treatable condition compared to MS, for goodness sake, and one that has not bothered me at all, whether due to the acidophilus or the general rebalancing of the system, I don't know.
The trouble is that a neurologist is not a specialist in antibiotics and most don't like to stray outside the accepted treatment options. Some GPs, who maybe know a little more about antibiotics, will give the go ahead for treatment, others won't. A possibility is that you ask your GP to write to my husband, as many GPs do in this country. His email can be found at the bottom of this page:
My neurologist would not have considered any of this treatment, but luckily I was married to the right specialist. He does now seem to be mellowing somewhat, in that he has admitted to David that my recovery was beyond all expectations.
It might be worth asking your neurologist also to get in touch with David, because there are now at least a couple in the London area who, although they leave the prescribing to David, do at least say that they can see no harm!
A few little edits due to the lateness of the hour when I wrote this originally.