I'd be very interested to hear what you find in the end as I have a similar clunk although I am coil sprung.
To check the splines on the gearbox do you need to drop the propshaft?
no, you open the round plate at the back of the transfer box and look inside the input gear.
chalk the wheels and take the handbrake off, and put the car in gear, ENGINE OFF, and raise one read wheel off the ground. you can then, by hand, rotate the prop or handbrake drum slightly and look at the backlash between the gear and the inner shaft (gearbox output shaft), there should be very very little or none.....