I'm sure you probably did but did you do the pin bushings as well? I don't know if you have your car on jacks stands but when I tried to align my car the first time it was on jack stands and the front of the frame sagged down a bit and that was a big issue with lining things up. I guess what I'm trying to say is if it's on stands make sure it's on the ground for a few hours or a day so it can settle out. This was a big help for me.
I have poly bushings and had to trim the mounts that sit between the door and fender to have the fenders meet the frame. It may not apply for your car but something to look at just in case.