I looked at the ZX6 linkage, it appears to me that the angle of those links is very important to get the correct rising rate...
Yes and no... The angle is less important than the horizontal distance between the upper and lower dogbone pivots (which, along with length, sets the angle). The progressive action is only one function of these linkages; the other more important function is that of multiplying the leverage of the spring upon the swingarm.
The progressive action is determined by the radius of the circular path taken by the lower shock mount (relative to the path taken by the swingarm, as measured in the same vertical plane), and the position of the mount throughout its stroke. In the ZX6 arrangement, this action is determined by the distances and relative positions described by the pivot points within the rocker link. As such, in my case I'm working hard to get the neutral sagged position of the rocker "just right".
...when in roughly the right position they would have to be spread out pretty far to clear the tire and that's what led to my question about how close the tire was on the left side.
The ZX6 dogbone links are mounted just far enough apart to clear the spring on either side, which puts their overall package width
just inside the tread width of my 120/90-18 tire. Go any wider (outside the tread width), and you begin to encounter chainline interference problems. Notwithstanding clearance for the spring, the dogbone links have to mount outboard in any event, as there just isn't enough room in the center of the swingarm; the crown of the tire tread is only about 7/8" away from the spring.
The upper mounts don't have to clear the sidewalls, moreover, it would be impossible with the stock swingarm. In my application, there turns out to be only one reasonable upper dogbone mounting location, and as luck would have it, it's both close to the stock-application geometry and clear of the tire
... It also seems to me that [the R1-style] link's length can be changed without goofing up the motion ratio as long as the relative angle is kept close.
Agreed, but... The relative angle is determined by both link length and pivot location; if you change the length without changing the pivot, the angle will change as well. This is why the best R1 lowering kits use different triangle plates, to change the pivot location along with the link length.
In adapting to the stock XS650 frame, especially with a stock(ish) swingarm, I've found that you're really limited in mounting options.
The R! system has merit, and I'd like to see it work. Besides, it keeps all the parts Yamaha!
I just couldn't figure out how do make it work for me.