Yes you DO have to have your foot on the brake pedal, because what people don't realise is that the first thing an EOL does is ANOTHER Clutch Drain Sequence at the start of the Calibration! It used to frustrate the crap out of me when I first started working on Alfas & Selespeeds as the EOL would pass/fail randomly, till I realised when it passed it was because it just so happened at the time I had my foot resting on the brake.
I know you've work on quite a number of them. But for me it was not required. Let me share my experience.
I've had a worn pump in the past and changing to a reconditioned one it works fine, the pressure is good since the accumulator is new. But calibration only works intermittently as you said. One day the pump only comes on intermittently. Thinking the pump must be bad I bought a brand new one and put it in. After that calibration works every single time. And I follows the instructions so brake pedal was never depressed.
The points I found very interesting were:
1. With the reconditioned pump the clutch drain procedure completes every single time. No fault.
2. With the calibration though, the pump will stop after a while as you know the calibration makes intensive use of the pump. If the pump is not able to keep up it will stop and throw a fault.
3. I opened up the reconditioned pump thinking I got conned. But there is plenty of carbon brush left and the commutator is in good condition.
I've not been able to explain why the reconditioned pump does not work well for the calibration.
it cant find 3rd and skips to gear 4 after short delay.
I've had this too. It was down to the big Selespeed harness connector near the battery. Cleaning the connector helps but in my case, actually some of the pin receptacles are not tight enough. The contact is still there but vibration might cause it to loosen a bit and throw an error from time to time. I bent the receptacles so that it 'bites' on the pin better. Never have any problem since.
Do check the pinch bolt too as suggested by Baz. Sometimes several kind of problems can give the same symptom so you'll need to check them one by one.