I drilled from the mark. That way I could ensure that the hole was where it was supposed to be, on the side where the position was critical. I have two 3/8" bits -- a brad point bit that came with my doweling set, and a perfectly ordinary 3/8" twist bit. Brad-point bits are far more precise than twist bits -- they're more likely to start where you want them to, and they're more likely to stay straight. My problem is that my brad-point bit wasn't long enough to go through 3-1/2" of wood. So I started each hole with the brad-point bit, then finished it off with the twist bit. I clamped a piece of ply on the back, to reduce tear-out.
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.
Once you have all the clamps on, take off the scraps of hardboard. You can clean up the glue squeezeout with a damp rag.. When the glue is dry, trim down the strip flush with the panel using a router and a flush-trim bit. Then cut off the ends of the strip with a flush-cut saw, and clean up with a block plane, an edge scraper, or a sanding block. Leaving the ends in place while you route the edge helps support the router.
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