Thanks for the tips. I have not gotten it aligned yet, I only test drove it a little today. I planned to wait until I had replaced all the parts before I get the alignment done. I used the Napa premium ceramic pads and Brembo rotors. Again, the brakes were fine for the past month after I replaced them, no shuddering. While it's possible they warped at some point, it would've had to warp while sitting in my driveway last night, since they were fine yesterday

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I did the front end work in stages. I did the right strut/strut bearing/sway bar link a few weeks ago. The left strut assembly and both outer tie rid ends was today. Now everything is in place and I'm going to take it for an alignment on Monday, hopefully that will fix it. I'll also ask the techs to check everything out, and make sure I did the work correctly. Maybe in that process the rotors will get reseated.
I'm wondering if the rotors aren't on there quite right because the new rotors were very loose on the wheel hub when I first installed them. I was thinking with all the banging and prying from replacing the tie rod ends, some rust got between one of the rotors and the wheel hub, making it out of alignment with the pads.