Jim,
The gear leg fairing alignment was a challenge for me. I had another post on this sometime in the recent past, but here is another explanation of my experience:
1) I originally "aligned" my fairings by just lining them up with Bob Snedaker's upper gear leg fairings. I supplemented using the Mark-1 Eyeball method, and they looked straight. However, my RV-6 came out with a very significant yaw when flying with the fairings on - so back to the drawing board.
2) I re-fit the fairings using the Van's string method, which was very confusing to me as well, at first. George's drawing should hopefully clear it up somewhat. That got me closer, but unfortunately did not take out all of the yaw. I still had nearly a full ball-width out of trim at cruise speeds. Back to the drawing board.
3) Third time, I used the trial-and-error method. I had a good place to start from using the string method, so I went from there. I had taken off the lower and upper fairings, so that meant I could adjust the leg fairings in small amounts to test the impact on flying qualities. I just marked where they were on the gear leg, then adjusted from there. Clamping down the hose clamp really tight kept them very securely in place. Then I just went flying and saw how it did. I was careful to be relatively consistent with my data points - same altitude and airspeed for each run. I found that I could take out the yaw, but the adjustment created some "heavy wing" when I did it. Makes sense, of course.
4) Another method I tried was to go flying with the hose clamps on a bit loose. I would fly the airplane up to redline airspeed (180kts, RV-6) and keep it straight with appropriate rudder. The idea was to have the fairings streamline to the relative wind, and see where they came out. This worked out OK - not perfectly. They gave me another datapoint for placing the fairings.
5) In the end, I found a happy medium, close to where the fairings streamlined, but not perfectly. They work a bit as a trim tab for yaw, but they give me a little bit of rolling moment as well. I wouldn't say I'm thrilled with the outcome, but they are functional.
YMMV,