After you have all the holes clean, set things up for your glue-up. You want everything on-hand before you start - drill, driver bit, glue, roller or whatever you're going to spread the glue with, and four clamps for the corners. You'll need a flat surface to do the glue-up on - I used my hollow core door on top my bench base - and another somewhat-flat surface to put the other panel on. My folding table was still holding my oak countertop, which makes a great flat surface, but I want to make sure I didn't drip glue on it so I covered it with some painters plastic that was left over from the last bedroom we painted.
If the holes of the first jaw are in the proper position, drill holes in the same locations on the other jaw. I lined the drilled jaw on top of the undrilled jaw, clamped things down, and then drilled about 1/4" into the undrilled jaw, to mark the location. Then I removed the drilled jaw and drilled out the marked locations the same way I did the first.
With the shelf secure, get a couple of friends to come help, and stand the bench on its feet. I said earlier moving the top by yourself is dangerous. Trying to lift the entire bench is foolhardy. Of course, I already said I'm stubborn, so I did it myself by rigging a simple block-and-tackle using lightweight pulleys I got at the hardware store. (Not the lightest-weight pulleys, those are meant for flag poles and have a design load of something like 40 pounds. These had a design load of 420 pounds.)

The base needs to be as wide as the sum of width of the guide strip and the distance from the edge of the shoe, plus a bit extra, With my saw, the overhang is 3-1/2", so I made my guide strip 5-1/2" wide. The distance between from the edge of the shoe to the blade is about 4-1/2", so the base needs to be at least 10" wide. Since I was working with a 24" wide sheet, I just sliced it down the middle.

So drill the benchdog holes through the MDF layer. Begin by laying out their positions. You'll want these to be precise, so that the distances between the holes are consistent. The vises you are using will constrain your benchdog spacing. My front vise worked most naturally with two rows of holes four inches apart, my end vise with two pairs of rows, with four inches between the rows and eight inches between the pairs. Because of this, I decided on a 4" by 4" pattern.

Synopsis: No room in the garage? Basement not an option? Consider what Ken St. Onge did when he needed shop space: He bought a prefabricated shed and converted it into his full-time woodshop. Because a pre-built shed doesn’t need a cement foundation and is built in a factory, it’s much less expensive than building an addition or stand-alone shop on your property. It can have taller ceilings than a garage and bigger doors than a basement, both big pluses for a woodworker. You can put a shed just about anywhere, too. Here’s a soup to nuts look at Ken’s experience, so you can gauge whether a shop in a shed is right for you.