Are the wheels aligned? A weave can start from a tight or loose steering stem. After installing often times they will need to be retightened a couple times. Are the shocks longer than stock, front end taller or shorter than stock? Spokes tight, tires seated properly, pressures correct? No fairing of any kind?
Did you have the S/A bushings made or did you buy them from a supplier? Some bushings tend to be slightly oversize. If I may I would suggest a different solution to torqueing the swingarm pivot bolt. With the shocks & wheel removed, and the pivot well greased, lift the arm to full travel top. Tighten the nut until the arm drops slowly (smoothly) under its own weight to the bottom of the travel. Often I found this method takes a bit more torque than Honda recommends.
Good luck, you'll find the cause.