Happy to say after a very frustrating 3 months I have finally fixed the issue.

Turns out that it was the PCM.

I had stripped out the entire engine loom, ohmed out all of the wires from the PCM to the various connectors, rerouted the loom and checked for any and all signs of rubbing, poor connections etc. Nothing.

Plugged in a 'new' PCM and problem gone.

I can only conclude that the overcharging alternator had managed to damage the PCM in some way.

Anyway. Fixed and onto the next issue!

Thanks to all that responded.

Paul