Clamp the inner jaw of the end vise in position, leaving a little bit to trim off later, and then use the dowel and dowel center trick through the screw and guiide rod holes of the vise base plate to mark the position of the screw and guide rod holes in the jaw. Remove the jaw and drill 1-1/8" holes in the marked positions. I used the drill guide for most of the holes, and drilled freehand for the last bit. When you're starting a spade bit in a deep hole like this, start the drill very slowly, and the bit will move the drill into a perpendicular position. Start it too fast and the bit will bind and you'll damage the sides of the hole.
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.
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.
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The next day, cut it flush. Use a block plane to ensure it truly is flush. This will be the top of the bottom layer of the bench top, so gouges aren't a problem. (Wiping up glue with a damp cloth can lead to stains and finishes applying unevenly. That won't be a problem here, either.) But bulges and bumps are a problem - they will keep the two layers of the top from matching up evenly.