Hey Pete.
I assume that your gear leg fairings are properly aligned first. This is more difficult than it seems, because it's possible to get a 'twist' top to bottom. I aligned mine using the technique
here (scroll down). Don't move or twist the gear leg fairings once aligned.
Once you align the gear leg fairing and attach the intersection fairing with fiberglass to the wheel pants, you can redrill and countersink for the attach bracket.
For me, one hole intersected the edge of the fairing a bit, but not as much as yours. Individual variation, I think.
Sorry, no pictures of my hole position.
One more thing... put several layers of reinforcement on the inside where the attach holes are in the wheel fairings. The stresses at these points are high, and when the e-glass wheel pants gets warm in the hot sun, they can deform and delaminate. I noticed that mine were deforming and had to add reinforcement after flying. I think I had a total of eight layers of BID.
Vern