CNC Design and advice

No problem with that.
I have seen some very nice work done on MDF routers and once you have a working machine it's far easier to make the MKII

My current design is based around 12mm thick MDF.

I have just been around to my local Sydenhams, and they stock MDF in the following thickness 9, 12, 15, 18, 22mm, they can also order in 25 and 30mm.

What thickness would you advice me to build the unit out of?

Thanks for your time.

18mm, it's only half as thick again and twice as strong.

Confidence is that feeling you get in the design stage. Suggest you get a bit of MDF, stick it in the vice and try bending it, you will find it goes easily one way and hard in the other. Right angle joints are your friends.

You started out designing a machine to cut PCB's and then, with an eye to the future, you enlarged it so you could make saucepans. You now have something that will do neither.

Strongly suggest you scale it back to cut chocolate box sizes. It should look chunky, the only thing on it that should look spindly is the spindle :beer: