Having never done POF before, I'll ask the newb question of how you came to realize your beams were crooked?
So, I noticed they were off because I happened to look down straight at it, like the below photo and noticed that the right side was much further back than the left.

This is how currently is. It appears the piece the fit into the bow is off somehow, or one of the first beams wasn't fitted right. It's hard to tell in this photo but the green circles show where the beams start to go crooked. This is the further I could go back without causing serious damage, so these ones are still off slightly.
Then the blue beam is still slightly off, the right is a tad to far back.
The red almost align perfectly with each other, but the beam as a whole seems to be too far a stern and doesn't align with the beam below it. From the drawing this looks like it may be correct, that this deck doesn't align perfectly with the deck below, but we'll see.
The other way to check alignment is the beams should connect to the same rib on both sides. So in the red circle you see how both sides of the beam touch in roughly the same exact location to the hull. You have to trust your ribs are correctly angled.