Scott --
Not being able to see a good top and side view pic of the LCA, I have to ask if they could possibly be reversed (wrong sides).
I have done initia lalignments like you are doing many times and had good success. There will be some compression of bushings with weight on the suspension, but it is negligable in the affect on the alignment settings.
As far as the lower shock mounting adapter is concerned, I would toss those mounts in the bin and make new ones, or at least cut off the ear that is too short and weld a longer one on to get the proper attitude of the lower shock bolt.
Is that the UCA that is resting on the chassis? If so, shim that up slightly.
You are doing well considering the hand you were dealt here.