Ok...
No MIL or error codes via a standard OBDii reader. Don't have access to a Hawkeye or similar.
When I first start the car, the gear changes are fine for roughly 5 minutes.
Then the changes become rough, in every gear except in/out of neutral.
If I stop and switch the ignition off and back on, the changes become smooth again for another 5 minutes or so.
One strange thing I have noticed is that kickdown is always smooth, but changing down due to deceleration is very rough. I avoid this be shifting into neutral before slowing down.
What do I mean by rough changes?
1-2 = thump from gearbox, sometimes takes 1 - 1.5 seconds for the revs to pick up
2-3 = noticeable hickup, i.e. car weight shifts forward then backward, ending in a thump, hard to tell where from
3-4 = thump from rear diff
4-5 = same as 4, not as violent
Before you ask, I haven't tried it with the propshaft off - I ruled this out because of the switch off/on thing.