I did finally get across to look at my sister's car on Tuesday, this week.
What I found was that there was a hole in the air pipework from the airbox to the rear of the engine. This was clearly shaped to take something.
On closer inspection I found a sensor lieing in front of the injectors, neatly placed. The shape of the end of this clearly matched the hole in the pipework so I have put it back there.
My thinking is that either this sensor (air temp sensor??) was getting wet and throwing the ECU or that water was getting to the MAF via the hole in the pipework.
Car hasn't been driven in the rain since, however, have been told by my sister it is running smoother.
Also found that when intercooler was replaced very cheap jubilee clips had been used and these weren't giving a seal on the pipes. My sister had complained of a whistle when she accelerated hard. Replaced these and again she has noted an improvement in performance.
Will be back if problem isn't sorted, but fingers crossed.
Thanks for all your help, on here and via PM.
Chris