Time to switch focus to the bench legs. I am pegging all of the mortises using 1/2 hard maple dowel rods. I use the technique called draw-boring. It is where you drill your hole through your mortise slightly off-set from your tenon, so that when you drive in the dowel it pulls the two pieces closer together. The resultant joint is going to be as tight as it gets for the long-haul, whatever abuse I dish out on the bench.
I have a flush-cutting hand saw that works well and fast for a few dowels, but I had 16 to flush-cut, so I reached for my Milwaukee oscillating tool to do the bulk work. Followed up by my flush-plane, and then a little super glue and sawdust to fill any gaps.
Now to fix the assorted screw-ups that came along the way. First off, plugged the random Domino mortise I cut in the wrong place:
Then cleaned out assorted glue squeeze-out in the routed groves with a chisel.
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