Did you try mapping caps lock as a control key, like on the Sun keyboards? Before I did this I had trouble with Emacs, but since then it's been perfect for me.
I found I had to actively train myself to use two-handed key chords. Right control-w, left control n, etc.
No more alternating nonsense. Pressing modifiers is instantaneous and requires no thought.
http://www.emacswiki.org/emacs/MovingTheCtrlKey
I ended up doing this on all three of Windows and Red Hat (work) and Mac once I got used to it.