Eric,
It sounds like the issue may be tied to a) getting "In" to "zero" and b) separating out the different workflow phases.
I find that my email inbox will grow to around 2000 items if I let it, but what keeps it manageable is a trusted archive and good search capability. Then get comfortable with having the calendar and tasks view be your primary focus when "Doing".
One exercise that may be helpful is to track your time - (I think this was discussed on the "Threefold Nature of Work" webinar)
-Mark