Eyeball,
There can be some play in the shock tower mounting screws when mounted to the bulkheads. Make sure the shock towers are level when mounted to the bulkheads as I've seen this type of issue throw off my car's tweak in the past.
Also, make sure the top edge of the lower spring collars are the same distance from the bottom edge of the lower ball joint. Sometimes the lower ball joints can have slight differences on their top surface and this can affect how high the lower collars sit on them. If there is a difference, then the top adjustable collar pairs will have to be moved out of alignment with each other in order to keep the same distance (and therefore spring pre-load) between the top and lower collars of both shocks. It really doesn't matter if one spring sits a little higher/lower than the other in a pair, as long as the pre-load distance between their respective collars is equal.
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