I did a power check on pin 85 and 86 on the ignition relay when when the problem comes on, and the switch power to the relay was flicking on and off with the ignition on.
As it's everything connected to that relay is flicking on and off I can't see how it can one of them causing the problem as it's the switch power that is going on and off and not just the individual component.
The engine was freshly built this winter, with new pretty much everything, it run for over 450 miles went for a tune at MSD but had a hole in the intercooler so couldn't do the full tune. The problem started on the way home and has been the bane of my life ever since.