I saw a similar gap between the main skins and LE skin. To make sure it wasn't due to poor fit from the ribs, etc, I simply clecoed on the LE skin without the ribs and still had the same, small gap. I can't see the wing right now, but I think the gap I ended up with was similiar to your quoted 0.025" value. By the way, your photo on the right seems to show the upper skin not aligned with the rivet holes in the spar.
Correction: I guess my memory's even worse than I thought. My bottom skins aren't riveted on, but on the top of the wing, which is riveted, the gap between the LE and main skin, and between the tank and main skin is less than 0.010" all along the span, except for a couple of spots here and there between rivets where a 0.010 feeler gauge made it all the way in to the spar. I think I remember that gap being larger before I riveted the skins (?)
I agree with the earlier comments about removing the blue stuff from the inside of the LE and smoothing the bumps at the edges of the flanges on the LE ribs; both suggestions make the fit much better and the assembly much easier.
John