Jez Harold this is turning into a real ball breaker!
The code erases itself upon restart.... it sets if you are getting into the secondaries, right?
It also sets if you are not into the secondaries?....do I read you correctly?
This stinks of an electrical gremlin if all the mechanical parts of the system pass muster like the guys are saying.
I intend no insult, you did run thru the diagnostic charts in the Helm FSM ? I know when I had my 61 it was a bit tough to do those charts as I didn't have a Tech1A and I had to use the alternate chart to use a DVOM and it was tedious at best for me. The one thing that I noticed using my snap-on scanner during my 61 episode was that when I used the "clear codes" option with the car at idle, the code would reset in a split second....which kind of made me think an electrical issue being at fault. I mean unless I had a leak in the sys the size of the grand canyon....how would it reset so fast? I think that if I was smart I would have concentrated on the electrical aspects based on what the scanner was trying to tell me....turned out to be my ECM.
Who did your ECM? I couldn't find anyone that wanted to work on mine....all I kept hearing was L98...okay, ZR-1....we will give it a shot.

Tom