Thanks for the response. The longeron was bent correctly; it turns out there's a lot of flexibility in the position of the aft end of the gusset, which means there's a lot of freedom in how you line up the aft-most hole. The forward-most hole doesn't move anywhere near as much as you rotate the gusset. In fact, yours exhibits a little of the same behavior, though nowhere near as bad as mine. In short: if you haven't done it yet, mark the holes, check the edge distance before drilling. Here's my solution, in case it helps out the next guy...
Vans wrote back and said they didn't know what caused the problem, but that I could just add a doubler. That didn't seem like a reasonable solution to me. Sure, I could add a doubler and put new holes in the longeron, but the new holes through the doubler would have bad edge distance in the gusset. I could add more holes way out in the gusset, but this wasn't satisfying to me, either.
After spending a lot of time playing with the parts and a sharpie, I realized that I could pivot the gusset outboard and fix the edge distance. For the right side (which I hadn't drilled yet), I went ahead and drilled through the side skin in the forward-most hole into the longeron so I could cleco to the skin and be sure that alignment was correct. Then, I simply squeezed the gusset inboard with my hands and drilled the aft-most hole first. Put a cleco in it, and drilled the rest. I think they came out just fine.
So, I rebuilt the left longeron with the bad holes (probably took me about the same amount of time as making a doubler from scratch, figuring out rivet lengths, etc, would have taken). Drilled the new longeron with my new technique and I think it too is now fine.
So, a note to anyone else who hasn't yet done this: check your edge distance before drilling these holes (particularly on the aft-most hole), and note that you can pull the gusset outboard as necessary to get the right edge distance.