I've rechecked the voltage between ground and the positive side of D3 and where there previously was 59v, there's now around 13v
That is actually fairly typical. The unloaded boost voltage you measured during the build process was before the VFD chip was installed. With the chip installed, it typically drops to the 12-16v range.
The two most likely suspects here are the tube and the VFD chip. We do test the tubes prior to shipment, but they are easily damaged by rough handling. Inspect the tube carefully and look for anything that looks like it might have been knocked loose inside.