I have completed 3 bikes in the last 5 months with the DVLA on the V55/5

You do not need to have valid insurance unless you are in Northern Ireland, the form is very clear on that specific point. You also do not need valid insurance for the first registration to get it taxed, weird but that is the way it is. subsequently you cant.

My bikes were all taxed on first registration but all of them didn't have insurance as they were stored at my local bike shop.

The Japanese registration certificate is down to individuals processing it, there is a long thread on another forum and horror story of the DVLA losing the original paperwork for the first V55/5, the owners had to go through many hoops to get it registered as the original japanese document was lost.