My advice? Don't do this. If you have jointer and a planer, use them. If you don't, seriously consider using dimensional lumber that has already been planed and sanded. If you are going to try to clean up construction lumber by hand, using a hand plane is a lot faster and more pleasant than using a belt sander. Except, of course, that to do a good job of planing a board you need a solid bench to hold the board, and you don't have a bench, yet.
Having done all this, I'm not sure I'd do it this way again. It might well be faster to layout the positions with compass and straightedge directly onto the top. Either way, you'll want to use a scribe rather than a pencil. Scribe lines are hard to see, and impossible to photograph, but the scribe and compass points click into them, allowing a precision that pencils simply cannot match.
Put the upper panel of MDF on your glue-up surface, bottom side up. Put the bottom panel of MDF on your other surface, bottom side down. (The panel with the holes drilled in it is the bottom panel, and the side that has the your layout diagram on it is the bottom side.) Chuck up in your drill the appropriate driver bit for the screws your using. Make sure you have a freshly-charged battery, and crank the speed down and the torque way down. You don't want to over-tighten the screws, MDF strips easily.
I marked out the one hole location, drilled a shallow 1/16" hole into the top. I then put a 1/16" bit through the hole in my template and into the hole I had just drilled. I lined up the template, and drilled a second hole, then put another bit through that. From then on, I worked entirely from the template. With two bits through the holes pinning the template in place, the other holes in the template would be precisely located (or so the theory goes) on a 4x4" grid.
This bench suffers from no such limitations as it provides an incredibly solid and stable workspace, albeit in a somewhat stripped down version. In terms of performance, Sjobergs tops our list at providing 80 lbs of weight capacity. This is one of the more quantifiable measurements to determine the quality of a work bench’s craftsmanship. This is achieved by using thick pieces of European birch wood and working it without using lower end joints – like butt joints.