I have had to change the viscous coupling on my sapphire 4x4 as it had basically burnt out, I don't know how long its being like that as I have only had the car 3 months and it only showed up when having a dyno run at MSD.
When the gearbox was out it was taken to a gearbox specialist to check it out and fit the viscous, they came back that the box was ok no problems
( there wasn't any that I knew about but just wanted it checking as it was out) now the box is back in with the new viscous fitted there is a really bad clunking noise coming from the back end of the box which was not there before when the old coupling was in so only running on 2wd, any ideas what it may be?

 

it can be the transfer chain jumping.

try and take off slow then boot it to see if you can hear the chain jumping.