For me, caffeine seems to have a direct effect on my stomach/esophogus, and a systemic effect. By that I mean that it's sympathethic properties causes more acid, I think.
I appreciate your dilemma. I have severe fatigue with my fibromyalgia, and caffeine seems to be the only thing that helps. I just have one drink in the morning, and so far, so good.
Here's what I do to help "soften the blow" of the caffeine. First of all, since I have alot of pain, I sometimes take exedrine free (with acetominophin instead of aspirin), and the effects of the caffeine on my stomach seem to be diminished. But I'd hate to recommend taking acetominophen, if you don't need it. Another thing I do sometimes is to take a rolaids tablet just before I drink the caffeine. It alkalinizes the stomach for a short while. I also think that calcium helps with my stomach problems too. But you certainly wouldn't want to do this with every caffeine drink during the day, because you could really mess up your electrolytes.
Today in the paper, I noticed an ad for a new coffee coming out, that says it's for people who have stomach problems with coffee. I think it's one of the major brands, like Maxwell House or Folgers. The big problem with coffee is that it is soooooo acidic, even when it's decafeinated.........so maybe this new type would help.
Another possibility for you is to give up the coffee, but take small doses of something like no-doz.........but be sure to read what the other ingredients are too.
Another possibility, which you probably aren't interested in, is slowly "detoxing" from caffeine altogether. I should do that myself......but I really think I'm addicted! I think caffeine can give us a rebound tiredness when it wears off........and we need another shot of it. But if you could take a month or so and learn to live without it, I'll bet your energy levels would rise on their own.
Also be sure that you are avoiding alot of refined products, white flour and sugar. Those can also make us very tired. Good luck!