Some more feedback:
After loading a new map, the bike started and idled for a full 15 minutes. This is the first time that I've managed to reach the 15min mark on the supposed reset procedure.
I took the bike out for a spin and there was a definite improvement on the throttle response, no stalling or hesitation when opening up full throttle from low revs etc. I stopped at Jo's place for a minute and switched the bike off.
When leaving, the bike started fine, road all of 100m to the first stop and then she died completely. No dash, no lights, nothing. While fidgeting with the battery connections, the bike lit up for a brief moment and then went dark again.

I took the battery out this morning and it held it's charge at 13.7V, so I'm suspecting another short or loose connection somewhere, probably likely to the multiple removal and re-fitment of the tank, battery, fuses etc. Or maybe the ignition.
But I don't think this new cut-out is related to the previous issue, so I have a feeling that we're moving in the right direction. Or maybe it's just my optimism getting the best of me...
