Good stuff. Note that there appear to be some 'burrs' on the locating pins, which, as you pointed out, are the probable cause of the slight gaps - pins not fully locating in the holes.
Going back to the rudder - that 'overlap' is actually part of the fin cap, and appears to have been moulded a part of the rudder in the kit, It will need to be sanded back some way to prevent an overscale 'bump', especially on the starboard side.