Ok so I took the SC to a different Pep Boys and told them the whole story. As soon as they got the car up on the lift one of the techs grabbed the service manager and told him he couldn't do an alignment on my car. So he brought me in the shop bay where my car was located and showed me extremely worn lower ball joints, the whole wheel on both sides lift up an inch or more. Hopefully this is the issue, I just picked up 2 new lower bj's and a bj press from advance. The guy at the second pep boys was awesome, told me to bring it back after i do the ball joints, they'll re align everything for free and make sure the steering wheel gets centered. Maybe I just never noticed the worn out bj's because of the bad strut rod bushings? I dunno..
From the description of how the car drives, it sounds like the alignment is messed up. But if the parts are as worn as you say, then the first shop had no business aligning it. Why did the guy at the first Pep Boys align the car when the ball joints were dangerously worn out? Wheel lifts up an inch or more? You mean if you pry between the ball joint and the spindle? That's insane. But not as insane as aligning the car that way.
(I have found that getting the cheapest alignment is usually the most expensive in the long run. Because they can't make any money if they do it properly, they put the newest, lowest-paid mechanic on it and hurry him through it. I would estimate that a proper 4-wheel alignment should take 1.5 to 3 hours. So multiply that by the shop rate and that's what a good alignment should cost. $100-$300 maybe, but certainly not $50.)
As for replacing the ball joints, since this is your daily driver, you need to be loaded for bear. You may have trouble separating the ball joint from the spindle. A pickle fork may not do it. But regardless of how you do it, you need to be sure that you can get the nut off the stud once you do break the spindle free. Otherwise, you will just spin the ball joint around and around, you can't loosen it, and you can't tighten it back up. Not fun. So remove the nuts all the way before you try breaking the ball joint free. (I recommend cleaning the threads before anything else.) Then put the nuts back on a couple threads to restrain the joint. Then you will have to pop out the ball joints. A pickle fork may or may not work. You may want to borrow or buy a ball joint separator and/or a large pitman arm puller. Like this:
http://www.zorotools.com/g/00057394/k-G0838187
or
http://www.tooldiscounter.com/ItemDisplay.cfm?lookup=OTC7314A
Also, if I recall correctly, in your first thread about the brake pull, the strut rod bushings were the first possibility brought up.
From the pictures, it's hard to tell how worn out the stock ones really are. Obviously, cracks in the rubber are not supposed to be there. But it's hard to say how much they would have contributed without seeing them in person.
As you can see, the aftermarket replacements are designed differently. They don't have any steel-to-rubber bonds, so they don't work quite the same way. I wouldn't be surprised if they changed the ride and handling of the car a little bit.