"I am pretty sure the alignment and azimuth were the same". Highly unlikely! When you replaced the screws you inevitably ended up changing the cartridge alignment and other performance parameters and THAT is likely responsible for 90% of the change you are hearing. Can screw materials, torque and some of the other variables mentioned impact the sound? Probably, but only slightly and it is doubtful you would hear it. The change in sound quality you describe is far too great to be accounted for by these variables. However, even the slightest change in alignment, azimuth, VTF will alter the sound in the way you describe.
cartridge headshell screws.
I cannot believe how much of a difference cartridge headshell screws affect the sound. I am currently using a Benz glider that was recently retipped. I was using a set of screws the retipper sent, then tried the VPI screws. Something did not sound right. Then I installed the original Benz screws and I'll be darned, amazing difference. They made all the difference. Incredible. Anyone else experience this?