Axel-
Good timing on this subject. I am finishing up my Phase I and just put my pants and gear fairings on a couple days ago. Per the manual, I aligned the fairings by string method, no weight on gear. Nevertheless, during flight I was definitely getting some roll/yaw forces (although this could have been due also to pant misalignment).
I waited to do the top/bottom intersection fairings, since I figured doing so would preclude me from adjusting the gear fairings based on flight tests. I'm glad I did so. After the first flight with fairings, I decided to do a flow viz experiment. I smeared engine oil along the leading edge of both fairings, then doped it with talcum powder, and went out and flew at cruise speed for an hour. When I returned, I had a very nice visual flow pattern that showed both fairings to be misaligned. Adjusted the fairings (TLAR method), redid the flow viz, and now the flow is straight and roll/yaw forces much reduced (there's not much I can do about wheel pant alignment at this point). I'm hoping the addition of the intersection fairings doesn't mess things back up again!
I'll post pics and a more detailed explanation on a dedicated thread in a couple of weeks when I have a bit more time. In any event, you may want to consider waiting to do the intersection fairings until once you've had a chance to fly the plane.
Eric