Now i'm confused. (since the PM's lol)
I thought the running engine was using a clocked wheel, didn't realise you'd got it running by swapping leads - if thats the case, then we know it works, you need to check & double check the non runner
Have you got (or access to) an oscilloscope to check if the VR is working ? Or are you seeing RPM when cranking ?
As said above, draw on some timing marks (the 4.6's don't have like the earlier models, but can be drawn with white pen) and see if / when it's sparking.
G