The rubber isolator should not be reinstalled with spherical bearing CC plates. One of the reasons for aftermarket CC plates is to accurately position the top of the strut for accurate alignment settings. Here's a shot of my MM plates:
As far as alignment goes, for a street car, go with -1* of camber, +4* to +5* of caster, and 0 toe.
Yes, the first pic is correct. But the reason for the spacers is to put the strut as high as possible (so you don't lose bump travel) without hitting the hood. Make sure you do that as bump travel is very important, especially for lowered SN-95's. If UPR's instruction's said to put the bigger spacer on bottom and 2 little ones on top, fine. But otherwise, make sure you get that strut as high as you can.
As far as the alignment, don't worry too much about it if you're getting it done within a couple days. Set the CC plates all the way forward and to the outside and you'll be fine. As long as you don't drive on it everyday for a couple weeks, you won't get any adverse tire wear.