Previously, I claimed that the pinion bearings are gone, but after reviewing the pictures and rereading the workshop manual's section that describes the axle rebuilding procedure, it occurs to me that what I observed (loose pinion) was expected because after you remove the flange, the outer bearing cone falls out. So, maybe the pinion bearings are fine after all.
Now, your response makes a lot of sense. Will do the test you're describing tomorrow. I hope the clunking noise is caused by the halfshaft splines on the inner side (the hub sides seemed to be OK). Since I just bought the truck, I'd like to run a complete set of maintenance first: replace fluids, grease whatever needed, timing belt etc. This is not the right time for dicking around with such a serious job as diff rebuilding.
BTW, why do you have to spread the axle? What's the point? Is it done to remove slack?