Cracked it. For the benefit of future generations of LS400 owners it was actually a hybrid (see what I did there?) of the various sets of rub your tummy/pat your head instructions floating around the t'interwebs. (I've amended the text)
These instructions work for an LS400 with a build date of July 1996 using remote fob 89742-50631 Happy days
1. Driver's door OPEN and unlocked, all other doors closed and locked.
2. Insert YOUR key in ignition, DO NOT TURN, remove key.
3. Using the lock/unlock button ON THE DRIVERS DOOR, slowly
press
lock and unlock 5 times (count the lock 5 times and unlock 5 times).
4. Shut door.
5. Open door.
6. Using the lock/unlock button ON THE DRIVERS DOOR, slowly press lock
and unlock 5 times (count the lock 5 times and unlock 5 times).
7. With the door open insert your key into the ignition, turn to on
position (DON'T START), wait 5 seconds. Turn off and remove key.
8. Locks should cycle once (Car will lock and then unlock once). If
they
don't cycle or they cycle more than once, do steps 1-7 over.
9. Now using the remote, push lock button, hold for one second,
release.
The locks should cycle once. If not, start over and go slower.
10. Close the door. Open the door. Press the lock button on the remote.
The locks should cycle. Close the door. Press the lock button on the
remote, the doors should lock. Press again and the doors should
unlock.
Just to be clear, the references to the button on the drivers door mean the central locking switch NOT the manual locking toggle next to the pull handle mentioned in other instructions out there.