I checked everything when I did the struts, all the control arms and control arm bushings are good. The 4 control arms bolt to a large sub-frame kind of thing thats held in by 4 bushing assemblies, that could be the problem. Those 8 subframe bushings cost $200. This is what they redesigned in later models.
My advice is to replace the strut cartridges, our 94's don't need wheel allignment afterwards and they are cheap. I bought KYB units for like $36 each. The upper strut mounts were $75 each from Lexus and weren't worn out, so I advise not to replace them unless they are bad.
I think I can live with the noise, it rides much better with the new struts now. I don't want to spend too much money on such an old car. I just replaced the radiator and hoses too.
Added picture of crossmember on 1994 ES300.