A couple of options
Here's some food for thought. One, another method for aligning the leg fairings is to mount your engine mount on a table and level it. Then, just drop plumb bobs on either side of the fairing. It's a piece of cake. Details are on my web site. Of course, if you are finishing up you don't want to unbolt your engine to do it, but if you can plan ahead, this is much easier than the string/plumb bob contraption that Van's calls for.
Two, I think (and fellow Rocket builder Tom Martin has some empherical data to support this) that the effect of fairing misalignment is somewhat over emphasized. While it might have a slight effect and slow you down maybe a knot, but not much more. Also, it doesn't really move the ball much either. Maybe they would if they were strengthened and had ribs in them, but as flexible fiberglass, they really can't push the airplane over much.
I know folks might disagree and I can't quote Tom's numbers, but he purposely flew with them out of alignment. Now, the Rocket fairings have twice the cord length as RV fairings, and he couldn't tell any difference.
It's always better to get them straight, but I suspect minor misalignments have little to no effect on whether your airplane will fly straight or fast.
Now, the vertical stabilizer.........that's a whole another story.