After some investigaton, it seems that the main spar flange bend angle isn't consistent along the length of the wing. Here, near the outboard end (rib 13, counting from inboard to outboard) I've laid my scale to show how the skin will transition from the ribs to the spar flange. It looks good. There's also no gap between the rib joggle flange and the spar flange.

...but here at rib 5, (the one with the .090 inch gap), laying my scale on the rib shows that the skin won't have a smooth transition from the ribs to the spar flange.

I decided to use my angle transfer tool to compare the bend angle at the two locations. Here I've set the angle at rib 13 and tightened down the thumbscrew.

...but when I hold it up to the flange at rib 5, the spar flange angle is significantly different. I took a measurement with a machinists protractor. The bend angle at rib 13 is about 90.8 degrees (i.e. the angle between the spar flange and spar web is 89.2 degrees). When I measured down at rib 5, I find that the bend angle is about 87.3 degrees (i.e. the angle between the spar flange and the spar web is 92.7 degrees). This means that the spar flange has been bent 3.5 degrees less at the rib 5 location than at the rib 13 location. I'm pretty sure this is the cause of the gap between the joggle flanges and the spar flange. I'll have to contact Van's about this. Maybe I'll make a posting on the list as well.