Wheel base difference side to side

Go back to your alignment guy. If he has a modern computerized system, he will have your workorder on file, and be able to call it up. Have him check the thrust angle. This will tell him where the problem lies.Only he can determine if shimming the spring is the correct thing to do.
Using the spindles, doesn't tell the whole story. Caster is often split to allow for a no-pull driving experience on crowned roads. Camber may not be identical. If the spindles are at different heights relative to a flat,level floor, and/or the rear axle centerlines are not the same height, the measurement will be off. And the clincher; there is almost no way to set the spindles to be exactly on the same transverse line.