I've had a similar issue with my MR going over speedbumps or potholes at low speed, literally checked everything and a mechanic at the local garage had exactly the same problem on his own Evo.
Personally I think It's a combination of the 'Anti roll bar clunking', that doesn't go away even if you change every bush or droplink and the 'floating torque transfer tube', that sits between the gearbox and transfer case, rattling.
Not to be confused with the backlash noise in the gearbox on deceleration, should you be running a racing clutch on a solid flywheel...
Just part of the Evolution experience.