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With this set-up the ride height will be higher: The YFZ shocks are longer and stiffer, that plus the extension will lift the bike up. Move the tabs outboard to set your preferred ride height.
The angle of the ball joint at ride height is not the issue, preventing the ball joints from binding at the upper and lower extremes of suspension motion is more important. IOW, the shock should be the limiting factor in suspension travel, not the ball joints. Angle the threaded slug to achieve this.
Now is also a good chance to set camber.
Read up on the Lonestar website on camber recommendations for your type of riding.
http://www.lsracing.com/img/Guide_21.pdf