Like a fool my alignment markings for putting the springs back together were not very good and wore off. Is the only key alignment when putting back rear the top spring perch the perch it self. Does it matter how the spring and the upper spring pad are oriented?

 

There are some minor alignment issues, if I remember correctly. There is orientation on the upper mount (the body mount is not perfectly square to the shock body), and the lower mount has the cone adapter to adapt to the lower trailing arm. I say minor because the shock shaft rotates, and you can therefore rotate the upper mount compared to the lower, but there is resistance because of the spring. You want to be pretty close when you put the springs back on, but it is not the end of the world if you are off a bit. Just be sure that the lower mount is aligned properly when you start the bolt so that you don't have cross-thread issues.

Mike