The first thing that comes to my mind is that MDF is actually quite porous. Air goes right through it when there is a pressure difference present across it. The factory top and bottom surfaces are heat sealed, but air will pass through the cut sides. You will have to heavily seal the edges, or use a different material.
You can, however, because of this, probably use MDF as the top surface of your vacuum jig, to "spread" your vacuum – as long as you machine the factory surfaces off the top and bottom. It's a fine choice as a spoil-board material anyhow, so it would seem to be great in this role.
Below the MDF spoil-board/vaccum "spreader," I would think about a fine array of holes or channels, rather than just a handful of 1" ones. You can get perforated metal sheet stock from McMaster-Carr, or use a table saw to cut a series of channels.
You could use loose sheets of thin neoprene to seal the areas that are not covered by the work, as needed (also available at McMaster-Carr). Theoretically, the vacuum will hold them in place, wherever you choose to place them.
Also, I looked up that air pump, and it pulls only 3.5 CFM. While I don't intimately know the details of vacuum engineering, I did have to learn basic principles of fluid dynamics, for my first career. And my gut says that 3.5 CFM just doesn't seem like enough flow to me, for an object that size. I believe you will have to upgrade your vacuum pump, or use it to experiment with smaller vacuum jigs.