The backlash in the diff shouldnt be an issue as slack is taken up as the right foot goes down. Would just cause an annoying thud. Could also be the indication of a worn diff.
My diff howls, creaks, grinds, whines and makes every worst possible noise imaginable. At low speeds it sounds like a train, at high speeds it sounds like my car has straight cut gears.
I have slop in the input flange (where the tailshaft connects to). I am assuming that this is causing misalignment of the pinion with the crown, causing a notchy vibration thats felt throughout the whole rear end of the car. (think bearings that have been preloaded too tight, that notchy gritty feeling). Since my problems occur at any speeds, they are most noticable at higher speeds since I cant really feel much in 1st and 2nd as the revs come up quick (tires let loose).
I am not saying this is your problem, but since this started happening when you swapped in the r200, maybe its worth checking out.
Check out the driveline angles first, obviously. Maybe the mounting of the r200 screwed them up somehow. You cant really do this by guessing, you need to measure the angles. Google driveline angles and youll find tons of sites explaining how. If you have an iphone you can download a sweet digital angle program for free of itunes, works great and is very accurate.
If your angles check out then pull out that diff and replace it with a known good one. Not worth rebuilding IMO, unless its an LSD.
Since youre running a rb25, you should really consider putting in an lsd. Since the longnose z31 lsd is impossible to find and very expensive, shortnose is the way to go. I am putting a GTR lsd with 4.11 into mine. Will cost me a few bucks but it is half the car after all.