Got a bit of an update, slightly inconclusive.
The explorer went in last week and had the ATF and filter changed, and the valve body gasket checked. (95,000kms on the clock)
The gasket was actually OK, it was replaced anyway along with the other standard gaskets in the kit (I think the servo and solenoid block gaskets). The valve body itself was resurfaced in case it was damaged.
I was happy enough to get the ATF changed, the replacement gaskets only cost me another $30 or so on top of the ATF and filter change so no great cost involved. The ATF was pretty gunky so I feel it was money well spent just to get that changed. Total bill NZ$540, about US$450.
Even though nothing was obviously fixed, the problem seems to have pretty much gone away! It shifts way more smoothly than it used to, and I have only felt the 'clunk' once in a weeks normal driving - and much less violent than before.
I now reckon the problem has been caused by a valve sticking occasionally and becoming free suddenly, or similar. The new fluid was significantly less viscous than the old, I think the better quality fluid has freed up whatever component was sticking and its all working more smoothly again.
One thing my transmission shop did tell me was that the Fords have frequent updates to the firmware in the computer that controls the transmission shifting. Normally these are picked up automatically and updated when Ford services the vehicle, but this one has never seen a ford mechanic since it was built - it has been serviced by non-ford places.
He reckoned it would be worth going to a ford place to get it checked for the latest updates, should only cost an hours labour. He couldnt do it for me as he didnt have the right equipment.
So I reckon my problem is about 75% resolved, I will get the firmware checked and call it quits for then. Once I put about another 30,000kms on the explorer I will get the ATF drained and replaced again as only about 2/3rds of the fluid would be changed so far, if I do the same again then only about 10% of the old fluid should still be left. Mercon V is kind of expensive though!