I bit the bullet and took my HD400 in to the Yamaha service centre. To cut a long story short: They can't fix it. "Spare part is not available". They were going to quote to replace the main PCB.
So, I have an HD400 that seems to be en route to the landfill as there is no way to get it fixed by Yamaha/Line 6.
Is there a service manual available that has circuit diagrams and diagnostic info? The technician said over the phone that the voltages on the main board were unstable.