Any recommendations on which 20 mm bit to use to make the holes? I will most likely be doing the holes with a hand drill and some sort of jig for alignment.
I am in the exact same situation as you are, and have done quite some research into how to create my own MFT workbench - maily because I don't need portability, and I am keen on making it a bit larger than the standard MFT.
A gentleman by the name of Peter Parfitt has a set of plans for an MFT style workbench, and I would point you in the direction of his YouTube channel, where there is much other good viewing.
As far as lining up and creating the holes in your MFT worktop, I have, after much research, settled on the Parf Guide system (you can find this at Lee Valley or Axminster tools). Again, Peter's YouTube channel has an in depth guide on using this wonderful invention.
You'll find his channel and resources here: http://www.youtube.com/user/StoneMessage/featured