I've now done the clutch rod adjustment (was over 29mm, now 28.3mm), and also installed the new crank sensor - thanks again IainFM.
Took the car for a test run tonight and the stalling/motor control system failure issues seem to have been solved - hurrah!!
BUT... the car is STILL missing 3rd gear going up through the box (happens in both city & manual). It seems to be "thinking about it" - there is a delay, and it then selects N or 5th - this seems worse when the car has been used for short trips or is hot.
When I got back I reattached alfadiag and tried the gear selection and, again, it woudln't select 3rd or 4th. I tried to do a recalibration, but this failed part way through.
I'm going to check for swarf in the end box at the weekend, but does anyone have any other ideas?