Is there an easier way of threading Technic pins into other elements?
As someone who also argues with LDD occasionally, have you tried using a placeholder technic beam to get two connectors at the right distance and then adding the axle into both connectors before deleting the placeholders?

If the placeholders are in a different colour from the rest of the model, you could use as many as you need and then delete them with the Colour Select tool, leaving just the parts behind.