Joe,

As far as the lift strut tubes are concerned, I'd go with the statement in the build manual black box which says "The lift struts must be absolutely straight....."

My kit was from the old defunct skystar company; and, I put considerable measuring of everything and modifications into the jury struts to make the jury struts perpendicular with the wing and the lift strut tubes absolutely straight, up and down, fore and aft. I ended up cutting the upper ends off the jury struts and welding in new sections of short tubes to make everything square and straight.

An engineer would be better equipped to give a perfect explanation why this instruction is critical; however, logic would seem to indicate a lift strut that is bowed would have less compression strength, like what a person would get with a negative G load like a hard landing or some interesting maneuvers.

I don't know that measuring off the fairings would be sufficiently precise compared to measuring off the LS tube.

Your measurements off the jury strut and the lift strut before the fairing is put on are what counts, providing the fasteners and clamps are in the same position as when rigged.