The doughnut is always deceptively soft and wobbly - I don't think it causes a clunk as you describe. If very worn it could let the bearing spin (but there'd be a rubber smell as you say) and at certain higher speeds I suppose it could let the prop go into an oscilation.
But you can easily test the bearing for whine by undoing the 4 bolts holding the support member and letting the prop drop. Then prise the doughnut off the ball race and you can spin it to listen for wear. If it merely whistles or moans a bit you can lubricate it by prising back the plastic card a fraction and injecting oil inside. I've successfully quietened a whining ball race with a high mileage and it was fine for another 100,000 miles.
The clunk/clack noise when you pull away after releasing the handbrake is the handbrake shoes suddenly freeing. They are floating rather than firmly attached to posts, prone to making noises if dirty or rusty, or breaking up. It would be worth checking inside the drum/disc and greasing the mechanism slightly.
Have you changed the gearbox oil recently/ever? I've found a tendency to whine can often be cured simply by fresh oil. Likewise the rear axle.
Check the prop shaft joints and the sliding bit carefully by pulling/twisting. There should be no movement in the hardy-spicer joints, and minimal at the slider.
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