I think the whining is pretty much normal, the gears in the transfercase are still 'meshed together' and whine as the speed rises. Once they loosen up again and 'slacken off' the whining goes away. At least thats my theory on it as my XJ does the same and has since I've owned it (35,000km now on 105,000km). I notice it particulary at higher speeds like above 70kmh and when accelerating hard, again it goes after a few KM's and wont come back until 4WD (low range in particular) has been used for a while.
The clunk can be the slipyoke on the rear driveshaft. Drop the shaft and give the joint a clean and a grease, I think this is pretty common as well
Cheers
Steve