I've been chasing this for a long time.
I've found numerous issues, and changed various parts, but its still there.
If your lucky its just the rear diff mountings. With mine, i upgraded the rear diff mountings and made everything nice and solidly mounted, and the problem got worse, with a really horrible metallic clank in 1st 2nd and 3rd gear when engaging the clutch.
I swapped the rear diff out for a spare, still the problem remained.
I've since swapped the gearbox, replaced a couple of CV's which had play in them, and swapped the upgraded rear diff mounts out for softer ones, which has made it less harsh and bareable, but STILL present.
Its most noticable now when lifting off the throttle or reapplying it once moving. These are typical symptoms of worn engine and box mounts, and usually you get the gearstick jumping around along with the thunk, but i've replaced/stiffened the engine and box mounts already, and the stick doesnt move at all, so the issue is elsewhere.
I suspect its a combination of issues all working together. Lots of little bits of slack, combining together and adding up. I know one of the front inner CV's still has a small amount of play, and i've not checked the rear CV's yet, but i suspect at least one of those has play in it too. It seemed to improve significantly when i fixed the play in the propshaft CV and swapped out the gearbox.