Nothing really to add to Daunted's post about the amoxicillin except to say that I have never taken it and you seem to be doing so well without it that it seems a bit superfluous.
(Edit on 06-09-06: Never taken it? What a fib! I did actually take it once for two weeks, after moving onto intermittent schedule, just to see what would happen - nothing.)
What I do want to comment on, though, is your reaction to the current hot weather: I was never particularly troubled by hot weather either, although our 'hot weather' is by and large nothing like yours, mainly in the 80's, rarely over 90 degrees for more than a few days at a time. When I discovered that I should be feeling drained all summer I was quite surprised.
However, since starting the antibiotics it is a different matter, but the reason seems to be that although MS causes a lot of mitochondrial damage, as soon as you start on the antibiotics, especially whilst taking flagyl, you undergo a kind of mitochondrial spring clean as all the waste products are cleared away.
When you take your supplements you might find it beneficial to increase the amount of the following: acetyl-l carnitine, alpha lipoic acid and coenzyme Q10 during the hot weather. Do a pub-med search on all of them.
Also you really should keep out of really strong sunlight whilst taking doxycycline.
The good news is that it won't be forever!