Thanks. I enjoy this stuff. Apparently I have no life.
As noted the shims are there to account for manufacturing tolerances and bushing positions. They are not used for alignment. Replacing the bushings will render the previous shim positions obsolete as its not likely that the replacements are of identical length or installed in the exact position. Also, I have never found a reason to have the shims in varying thickness unless it makes installation easier at the factory.
I think I posted this a long time ago but I couldn't find it. The process is pretty simple. With the car on jack stands install the control arm (no shims) with just the bolt in position (no nut). Place a stand under the end of the control arm so it is near normal ride height (with the ball joint about the same height as the inner pivots). Move the arm through its range of motion to ensure its not binding at the normal ride height position.
Center the rear pivot between the body mounts and check the forward pivot to see if it is similarly positioned (it is likely biased to one end or the other). Now adjust the position of the arm fore/aft to equalize the bushing locations to have both as close to the center as possible. With the arm now centered use a dial caliper to measure the gap between each side of the bushing at the rear pivot. Or you can just assemble a stack of shims and try to fit them into the gap until you find a stack height that fits.
With two stacks of shims for the rear bushing ready, pull the bolt and insert a stack on the rear most side of the bushing, insert the bolt to about half depth and repeat for the other side of the bushing. With the bolt in place check the rear control arm pivot for axial movement (movement along the axis of the bolt or simply 'fore/aft'). It should be snug but not tight. Repeat the procedure for the front pivot. Once both pivots are shimmed on both sides again check each control arm pivot for axial movement. Assuming they are good remove the jack stand and check the control arm for range of motion. It should move the same as before the shims were installed.
Finally; replace the stand under the ball joint to position the control arm at ride height and torque the pivot bolts to spec.
Note: I put a light coating of anti-seize on the pivot bolt and all of the shims. This will keep them from seizing in the bushings. I had to use a sawzall to cut a pivot bolt to get a control arm out once. Never again. And I have seen the shims get rusty and chewed up.
Hope this helps.