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.
With my second attempt at edge guides, I made the other rough-cut. On this, the edge guide worked fine, but the end of the cuts revealed that the saw blade wasn't quite square. So I adjusted the blade, clamped all four legs together, and made what would be the first final cut, if it came out clean enough. It didn't. I'd let the saw drift a bit away from the guide edge. So I adjusted the saw, moving the guide back half an inch, and tried again. the rough-cut parts were a couple of inches longer than they needed to be, so I had room to work with,. It's only the final cut at the other end that you only have one chance at.
Well, not these plans. You have the option of building a very functional and spacious lean-to shed on different foundations. Your foundation choices are: concrete slab, a wooden floor supported by concrete piers, or a wooden floor supported by skids. That lost option also means that your lean-to could be mobile as well so you won’t have to decide where you want to permanently put it.
Thread the rods through one of the legs, then set the leg flat on the table. Insert dowels into the dowel holes. Place the matching stretchers into place. Put dowels into the dowel holes at the top end of the stretchers. Place the other leg onto the threaded rod and settle it down onto the dowels. You'll probably have another opportunity to whack away with your rubber mallet.
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With the inner jaw fastened to the bench, I used the router to flush-trim the jaw to the benchtop, across the top and down the sides adjacent to the top (stopping short of the discontinuity between the top and the legs). I'd thought this would be the best way to match up the jaw against the top, but I'd not do it this way again. It was very difficult to hold the router tight against the face of the jaw, and the result was a surface that wasn't as even as I had hoped.
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Cut 15 top boards 5 ft. long and rip them to 3 in. wide with a table saw so the top will glue up flat without the typical rounded edges of 2x4s. For the leg slot, cut two of the top boards into three pieces: a 39-in. middle piece and two 7-in. end pieces. Glue and screw the top together, one board at a time, with 3-in. deck screws, keeping the ripped edge facing up and level with the adjoining boards. Use a corded drill so there’s plenty of oomph to drive each screw below the surface. Note that the third glue-up from each end is where each leg notch is inserted. You can also create a nifty tool tray in the top by notching the three top pieces with a jigsaw. Clamp every 8 in. or so before driving in the 3-in.deck screws. Predrill the screw holes near the ends to prevent splitting. When you’re screwing on the 7-in. long 2x4s to create the leg slots, use a scrap piece of 2×4 as a spacer.
The holes we want to mark are the holes through which the threaded rod connecting the two legs will run. This threaded rod will run through the 3/8" groove along the bottom of the short stretchers,. The hole for the upper stretcher has to be positioned so that when the rod is running through this groove, the top of the short stretcher is even with the top of the legs. The most precise way I've found for marking the position of this hole is to use a dowel center. Fit the dowel center into the bottom groove, line up the stretcher, and bang on the end with a rubber mallet. The dowel center will leave a mark indicating the center of the hole.
When the top is done, we want the edged MDF and the oak countertop to have exactly the same dimensions, and for their width to exactly match the width of the base.I could see three ways of doing this: 1, join the MDF to the countertop and use my belt sander to sand down their joined edges to match the base; 2, join the MDF to the countertop and use a hand plane to plane down their joined edges to match the base; or 3, use a flush-trim bit against a straight edge to route the MDF to the width of the base, then join the MDF to the countertop and use the flush-trim bit to route the countertop to match the MDF.
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.

Something like this really does look like it would be a fun project. I guess I need to go out to the yard and use some stakes and brightly colored taped to mark off some different dimensions (12x8, 12x10, 12x12, etc.) to figure out just how big I can make this thing. If I'm building it myself, it'll be easy to keep the height right at the 9 foot limit.

I agree that I might quickly outgrow a 12x8 shed. Lowes also offers a 12x10 Rancher (same style, but more room), but the 12x10 is 9 feet, 4 inches high, and my community only allows a maximum height of 9 feet. The 12x8 is exactly 9 feet high. I'm afraid of getting "out of spec" if I exceed the height limit and then getting in trouble with the Home Owner's Association. Having said that, 12x10 would be about the biggest size I could get for the available area in my back yard, so even if I hire a shed contractor to do this, the shed would have to be 12x10 or smaller.