[wraith]

Why do you think its backlash causing the clunk? When your moving and applying power, the driveshaft can move up and down also at the joints, the rear diff can tilt if its got worn supports, the motor mounts could be worn out allowing the whole transaxle to tip and turn which could also make the driveshaft wobble. You see, the reason I say this is that your talking MM of backlash and having measured my back lash at the diff housing versus the companion flange, I have about 0.5 inches of play turning from one side to another and my car only clunks when I take up the slack in first gear at a light. However, I have owned my car forever, and its done that since it had 30k miles and still does the same thing at 126k miles. My POntiac GTO has a multi-link driveshaft also, and it never made a sound when it was brand new but 10k miles down the line, I started hearing a clunk but again only on initial driveline take-up off the line or moving while off the clutch and back on. Neither car clunks or vibrates once its in gear and accelerating. The VR-4 will occasionally (if my tune is a little off in first gear) surge in 1st and the car will jerk but it did that when I had a small vacuum leak and the car was BPU about 6 years ago. I have since fixed the surge thru tuning and that jerk is gone now.
I think you should get the car up on a lift and have some one get it in gear and try different things like pull the parking brake and give it a little clutch to see if anything tilts or moves in a way that shows where a bushing or a bolt is missing or loose.
When my car was new, the guys at MItsu had it up on the rack to check the VCU and they put it in gear and let it run in idle and the wheels would not turn smooth but with a jerky clunky movement (rythemically with the drivetrain slop), and they said that was normal. The cars just got alot of slop when you add up all the joints and components.