I figured out my misalignment problem. This vertical peice was built exactly according to the plans in metric. But apparently it was supposed to be as wide as those two 3/4 inch boards underneath it. I guess metric lumber is thinner than the US lumber I used.
So I just need to cut a 9mm thick shim to go in there. And things should line up.
Although maybe that will mess up the blade guide fit. I need to ponder this.