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I have read lots of posts on the threaded rod method to compress the spring, but on the install, is the spring seated in the lower control arm with the control arm attached or not? I tried several methods over the weekend and was not able to get the spring to seat in the upper housing. Yes, I used the pry bar and tried to pry it over, with lots of effort, thought I was going to rip it from the jacks! (It did not help that my NEW SEARS floor jack did not work. Would not lift a 12 pack! This was a repalacement for another new failed floor jack! Thank God I did not use it for removal.) My springs were really hard removing, they had a terrible bend even after the lower arm was lowered.
I did the same thing you were doing, using the threaded rod method and compressing the springs. IT worked OK to get them out, but could NOT align the upper arm, either. I had a floor jack and "manual" tools, also. Ended up taking it to my local mechanic and he had it together in about ten minutes. The advantage of 1) experience and 2) the right tools.
It took me a couple of times to get the top lined up correctly, just be patient. I put the spring in the lower control arm, then the top and slowly jacked the lower control arm up until I could get the spindle connected. It is hard to tell that the spring did not sit in the pockets right until you install the wheel and put it back down on the ground. Discovered this, took wheel back off, spindle back off lowered control arm back down, rotated spring a little bit and then put everything back on. Second side went in in about 10 minutes.