Nevermind got the measurements... thanks!
OK, here is stock 250r frame with stock 04-05 swingarm with stock 04-05 dogbone and linkage:

On the graph, from left to right bottom axis is full droop to full compression of the shock and the Y axis is the leverage ratio, leverage ratio is a curve not a single number, its the change in wheel travel divided by the change in shock length. I've been setting preload length at half of the travel, good or bad, its just a starting point for now. The orange curve represents stock 08 450r geometry, however, I wasn't 100% sure what parts I had at the time, so take that with a grain of salt for now.
I set the frame at 1" off the ground for full compression, and 13" off the ground for full droop. You'll see right around the 9.5" mark of shock compression the linkage nearly goes over center that is why there is issue with the curve, i.e. bad.
Dashed blue line represents the shock, the red lines represent the swingarm, dogbone, and linkage. This is at the 10" of compression you'll see the dogbone and link are nearly in a straight line so that is causing out problems.

So lets try a few things to correct it.