The majority of the mdf in the JOES2006 build is 1/2". Some 3/4" in the Z axis carriage and some HDPE involved in the bearing supports. Here in AUS, our mdf is 12 & 18mm (plus whatever humidity level you're building in.....) so you have no choice but to customise the build somewhat. Plus you need to work out if you're going to have the parts manufactured, or make each piece yourself.
You have access to sooooooo many informitive threads on this cnczone that you can find yourself going around in circles. Eventually you just need to commence you're own build and modify/adjust your plans a you go.
At least check out JOE'S original build thread on the 2006 to get a good idea of all the parts involved (lots of good photos too). Mind you, that thread is almost 1700 replies long, so don't expect to cover it all in 1 night!!!