I made a template by scribing two adjoining squares on a piece of MDF, using compass and straightedge, then marking each corner with a centerpunch, then drilling the points with a 1/16" bit. I find I'm always breaking small bits, so I picked up a couple of each size some months ago, and on looking I found I had three 1/16" bits, which worked fine for what I intended.

You're not the first person to say this! I'm half inclined to use the Lowes shed as a starting point for my own design. But I do think I'd feel better if I could work as an "aprentice" next to an "old master". Someone at work is going to put me in touch with a guy who builds sheds for a living, and apparently he's competitive with the prices @ Lowes and HD. The Lowes shed comes with a "Handman Package" that I don't want but would end up paying for, anyway. The "workbenches" were laughably flimsy.

My first attempt at making a cutting guide didn't work. What I ended up with worked fine for cutting panels, but the guide-strip was too narrow, and when the saw was extended fully for rough-cutting the 4x4's the clamp heads got in the way. So I made another. Actually, I made two more, so that I could cut one into shorter pieces that would be easier to handle.
Regardless of which type of screw you use, you'll need to flip the panel and use a countersink drill to on all of the exit holes. Drilling MDF leaves bumps, the countersink bit will remove them, and will create a little bit of space for material drawn up by the screw from the second sheet of MDF. You want to remove anything that might keep the two panels from mating up flat. I set a block plane to a very shallow bite and ran it over what was left of the bumps and over the edges. The edges of MDF can be bulged by by sawing or just by handling, and you want to knock that down.
In terms of size, this bench is another Sjobergs that is a bit on the small side, though it is actually far more squared than some others. While its length is a bit disappointing at 54″, the width is over 24″ wide which does provide for more diverse projects. Even better, this product still features the incredibly 500-pound weight capacity and continues the Sjobergs trend of avoiding joints that are not as durable as they otherwise could be.
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Permanent or Portable? This is a distinction that decides much about your bench choice: Is it to remain stationary or must it fold, roll, or otherwise make itself scarce between jobs? Large, heavy benches are more stable and, in general, more adaptable to different jobs (sometimes several at once). But the bigger the bench, the more hassle involved with stowing it.

Out of all the shed books I have read, this book stays by my side while I hammer in the yard. The book is well written by what appears to be a non professional book writer (A Good Thing). It reads as if you are getting advise in laymans terms from your neighbor "The Craftsman", a welcome change from the DIY books, that assume a level of expertese. The level of detail is high and discusses gotcha's, advise, and trade "secrets" that could have only come from years of personal experience building sheds.