A woodworker's workbench isn't a table, it's a work-holding system. It's not something you set things on top of, it's a tool that holds your work. Where a worktable might have a machinist's vise bolted to its top, a woodworker's bench is built to accommodate a number of different workholding mechanisms, such as bench dogs, planing stops, hold fasts, or board jacks, and will usually have one more woodworker's vises integrated into its structure.
Put the countertop on the base, put the MDF on top of the countertop, and line up the marks you drew on each end of the MDF with the countertop below it. When you have it lined up, clamp things down, and route the edge of the MDF using a 1-1/2" or longer flush-trim bit, with the depth adjusted so the bearing rides on the countertop. I clamped a couple of scraps of doubled MDF at each end to give the router base something extra to ride on at the ends.
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As I was handling the 2x4's, during the routing, I realized that I really wouldn't be happy with the look of the bench, if it were made from these unfinished boards. They had stamps, pencil marks, and more importantly, incipient splinters left by the saw, none of which I wanted. And I was remembering what other shop furniture made from unfinished pine had looked like, after a few years in the grime of a shop.
Proportion is the correlative relationship of all the parts to the whole. Although proportion usually refers to size, it is also a way to compare harmony between colour, quantity, placement and degree. Proportion is achieved when all sizes, shapes, textures, colors and so on complement one another. Remember that the eye appreciates some differences and may find equal parts monotonous and boring. Dividing space into equal parts such as halves, quarters and thirds is predictable and as a result the eye often skips past it.
Of course, I, on the other hand, with my Ikea oak countertop, probable went overboard in the other direction. Since I needed to trim the countertop to width,I figured I'd take off a couple of 1/2" strips to use for edging the MDF. I clamped the countertop to my bench base, and used the long cutting guide. I'd asked around for advice on cutting this large a piece of oak, and was told to try a Freud Diablo 40-tooth blade in my circular saw. I found one at my local home center, at a reasonable price, and it worked very well.
With the top laying on the floor, bottom side up, the next step is to flip the base upside down, and attach it to the top. I followed Asa Christiana's design, in using s-clips. When I stopped by my local Woodcraft, though, they only had two packages of ten, so I didn't use as many as I would have, otherwise. For the top I put four on each side and two on each end. For the shelf I put three on each side and two on each end. If it turns out that I need more, I can always add more.
The reason I'd cut out the rectangles in the vise support was that I'd intended to put a benchdog hole through each, and I wanted the thickness of the top to be the same for all of the benchdog holes. Where I messed up was in not cutting out the ends, between the bolt tabs. I'd intended to put a benchdog hole through there, as well, but I'd forgotten to cut out the segments prior to glue0up.

I decided to finish the top with a number of coats of Danish oil, followed by a coat of wax. I applied the first coat of oil in the usual manner, making sure to cover the edges, and down the holes. I applied a coat oil to the top side of the shelf, as well. Wipe it on, let it sit wet for half-an-hour, then rub it off. Wait a day or two, add a second coat, and then again for a third.
For one, the bench itself is a good size. While its width as a tad short at just over 1 ½’, the length is a great 5’ long. Even better, this bench is made out of birch wood. Birchwood is similar to beech in that it is strong but soft enough to prevent inadvertent dulling of your tools. However, birch has a bit of an advantage over beech in that it is not a porous which makes staining on the Windsor Design a more worry-free affair.