Do you have a table mounted router? If so then because you want to make the dado cut 2" apart I would cut them like making the box joint.
Increase the distance between the fence and the router bit to 2" instead of 1/4". Cut first dado then put the cut dado over on top of the fence and make the second cut. repeat this operation until you have all of the cuts made.
I would make the sides as one piece, rout the dados in the piece then cut the piece in half to make the two sides.
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