Once you put some weight on the front end, the spring pockets will align and the bow in the springs will go away. The shock should not act as a bumpstop either for droop or compression, and the lower control arm should be parallel to the ground with the full weight on the car. The CE top spring pockets should have adjusters to allow for a small amount of ride height adjustment.
I think you're coming along just fine. Once you get it all together, then take another look at it and see what the springs look like.