Some really amazing advice and words of wisdom, thank you so much guys.

I had a go at mocking up a couple of components in ply and it was useful to help visualise assemblies before commiting to cutting aluminium. That was a while back and since then my CAD skills have moved on a bit so I am more inclined to model it in CAD now than in MDF or ply (although sometimes it would definately be quicker to just go and knock out the part in ply!).

I will certainly be using CAD with a different midset going forward. Back when my CAD skills were very limited I was using it as a way to visualise the overall machine and give me an idea of what the finished thing would look like. From the advice here I can see now how it's real power is the ability to precisely model the real world and to resolve issues and conflicts before I go anywhere near a power tool.

Looks like I'll be spending this rainy weekend in front of the computer and trying to lock down the design as much I can. I'm really itching to get started with the build but I now appreciate how much time and heartache can be saved by spending the time on the design (although it is starting to annoy Mrs Barnacles - every time she walks past I'm staring intensely at a virtual CNC router. I told her it would only take a few weeks to build, that was over two years ago!).