Like the others, I too had trouble here. Not sure how many times I cleco'd and uncleco'd that assembly. Double checked to see if I had the left lapping over the right etc. My assembly looked exactly like yours.
In the end I found that it just took a ton of massaging. I know that's not what you want to hear because we're not really sure what that means....but it worked. I made sure the skeleton underneath the skins was correct, took the first 6-8 clecos out of the sides, squeezed the skins for all I was worth, did whatever I could to get a cleco through both pieces.
Once I got a cleco through both pieces (will be at an angle at first), used a bit of leverage to line the holes up. Since the front of the rudder has a very slight radius, the cleco's will be at a small angle (outward) even when everything is properly lined up.
Short version: It will go, use patience and tenacity.
By the way, I don't think the plans all for it, but it might be a good idea to put a slight break on the overlapping skin.