I've been taking my entire daily dose of doxycycline (400 mg) at once, in the morning, with breakfast. And it's going pretty good so far! Yesterday I didn't have enough to eat, and I was pretty nauseated for a little while, but it passed.
And I'm not getting the weird side effects from the ceftriaxone in the evening. So perhaps it was just the doxy + ceftriaxone at the same time that was giving me grief.
Finally, I'm still waiting to hear back from my LLMD regarding my questions about Plaquenil.