Wow..I'm a little stressed out after reading that!
I wouldn't worry to much about the 3/4" diff in height at this point. Seems to be a common problem when installing new leafs. It drove me nuts trying to get mine right. Biggest mistake is putting the car on the ground with all the nuts and bolts tightened. It also could be that one leaf has a different arch than the other.
The other issue is confusing...clear as mud kind of thing. Did you use the DSE Offset Shackles? Do you need them?
Keep the faith. Someone here has a solution.