That is exactly what I did last night. I had the adjustable lower CA's shortened from the (stock) length of 18 1/2'' down to 18'' in order to correct the pinion angle with the stock non-adjustable upper.
Now that I have an adjustable upper, I lengthened the lower CA's back out to 18 3/8'' (near stock length) and shortened the adjustable upper CA to get my pinion back to -2/3 degrees. Took a long test drive last night and everything seems to be adjusted perfectly now. I knew what to do with the panhard as far as correcting axle alignment, just not about the upper/lower CA's.
I guess it's not rocket science

but I was wondering where to begin with it!