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I drilled the hinge holes 1/4" from the back edge of the hinge half which is essentially the center line of the hinge but when they are attached to the existing holes in the spar the hinge pin protrudes about an 1/8" past the rear edge of the spar and skin. A detail on the plans depicts the hinge pin being centered under the edge of the spar. It obviously can't be in that location if the hinge is drilled according to the plans. Anyone else run into this situation or am I not interpreting something right?

Are you sure you used the P3 hinge. If you used the P4 hinge, that would move the hinge lugs aft. Check the stamping on the hinge.

Yes I used the MW20257-3. The plans actually call for MS20257P3 which is what the tag on the hinge bundle says but the hinge stamp doesn't have a P in the number.
The 20257-4 is about a 1/8" wider which if drilled as shown would put them even further beyond the rear spar edge. If I place the #3 hinge so that the pin is centered with the aft edge then the holes are 3/8" from the back edge of the hinge, not 1/4" per plans. I'm at a loss on this one. Something is out of whack.

I didn't drill the holes in my hinges until they were test fit on the wing to establish the proper fit and drill location line. Clamped the hinge in place. Then drilled and clecoed a couple of holes on the ends and the center to hold the hinge in place using the pilot holes in the skin as a guide. I test fit the flap at this point to see if the fit looked good. Then I finished drilling the rest of the holes starting near the established clecos and adding more clecos as you go always using the pilot holes in the skin as a guide. My flap ended up fitting well using this method. You may want to buy some more hinge stock and give this method a try.

Check out my thread around here:
viewtopic.php?f=39&t=578&start=820

IIRC, there were already holes in the trailing edge and I clamped the hinge so it was lined up the way I wanted. Then I transferred the holes. I think I did this just to the aft spar or skin before the wing was assembled.

Also check out this page. My rivets are close to the hinge loops.
viewtopic.php?f=39&t=578&start=690

Look for the post that starts with the pancake drill, picture that has a tipped over decaf coffee can in it.

Bryan Cotton wrote:IIRC, there were already holes in the trailing edge and I clamped the hinge so it was lined up the way I wanted. Then I transferred the holes. I think I did this just to the aft spar or skin before the wing was assembled.

This is also what I did IIRC. Wingnut (OP), can you reference the plans page you're working from? My recollection is that the wing skin as well as the rear spar already have pilot holes from the kit, so there's no need to pre-drill the aileron and flap hinges that attach to the rear spar prior to fitment. Instead, you position the piano hinge at the appropriate location on the aft spar and clamp in place, then use the existing rear spar/skin holes as guides to pilot drill the piano hinge.

Since you're on the topic of fitting flap hinges, I think it's important to mention something I encountered. The final alignment I had with my flaps resulted in the top surface of my left flap being flush with the top of the wing skin, but my right flap was slightly proud of the top of the wing skin. This ended up preventing the right flap from "flexing" up and under the top wing skin under aerodynamic load, and my first flights ended up having a fairly pronounced left-wing heavy feel. I ended up drilling out the piano hinges on my right flap and adjusting its position such that the top of it could "slide" under the top wing skin when under pressure and this fixed my heavy-wing problem. I suppose my takeaway from this is to make sure that the top of each flap (left and right) is the same, either they're both proud (fully stopped by the skin) or both have the ability to "tuck" under the top skin at the rounded top edge.

Thanks for the feedback. I predilled the hinge per plans on the first wing and everything seemed good but apparently I didn't notice the detail about the pin being in alignment with the edge of the spar and skin. The other day I referred back to the plans before mounting the spar hinge to the other wing and noticed the detail. I looked at the completed wing and that pin didn't align with the spar but seemed ok otherwise but apparently I saw the detail when I did the aileron and must have clamped the hinge to the spar and drilled it that way because it's correct although the back edge of the flap extends further than aileron which makes sense.
I've done the hinge that way on the 2nd wing already and the holes are closer to the hinge barrel's than the plans call for but the pin is where it's supposed to be. Guess I'll have to drill the flap hinge rivets out on the first wing and replace the hinge. You'd think Sonex would have run into this situation before and changed the instructions. It should have you predrill the flap and aileron half of the hinge and clamp the hinge to the spar and use it as a guide to drill the correct position of the other half of the hinge so they are in the correct position.

I'm curious what you have for a dimension from the edge of the skin/spar to the center of the rivet holes. Mine were very close using the drill first, ask questions later method.

It's hard to imagine there would be that much difference between factory spars and skins. (I'm sorry, did I say that out loud?)

It seems that there are several occasions when you have to ignore one set of details and go with what results in the correct final outcome. All they would have to do in this case is instruct the builder to clamp the spar hinge to the spar per pin location and then drill the holes using the spar holes as a guide. The plans clearly call for both hinge halves to have the holes in the same location.