Are you using a plunge or fixed based router? A plunge would make your project simpler. In any case I suggest you make a simple straight edge jig that you can clamp to the ends of the project or somewhere on the work table. Set the router bit into the each hole made then mark 90° from the outside edge of the router base. Place the straight edge to the marks made and clamp it down.
I would choose 2X stock or something thick enough to allow you to tip the router down into the eventual dado track
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