I'll tell you what has kinda-sorta been working for me (us) recently.
WAW and I have the same problem -- constant misinterpretation of meaning, even in written comms (particularly in written comms) -- because (in my POV) we're both intensely suspicious of each other.
So I have taken to writing in what is an admittedly irritating, but not at all misinterpretable, form of dull-as-dishwater writing.
I do only facts. I take out all modifiers (-ly forms, etc.). Every thought / response / question gets its own line -- no paragraphs. And I start every single one with "I state that..."
According to her it bugs the crap out of her -- hell, it bugs the crap outta me -- but I've noticed that her responses have become infinitely more moderate, focused, specific, and (if one can mind-read for a skosh) "balanced."
When she replies (if a reply is needed), she has taken to cutting-and-pasting the (my) original text and then following it with her reply to that specific point.
I have followed her example and done the same.
At the end of it you get these incredibly convoluted looking e-mail chains, but also direct and to the point responses.
And by taking all the modifiers out ("totally," "absolutely," "unbelievably"), all the emotion gets washed out, too.
