To follow up on Markd51's comments I use a MintLP Tractor with my Scout, JMW9 arm and Dynavector 20X L cartridge. It's a very exacting procedure and takes some time to do it right but I have not had any of the issues the OP is having. I use the twisted tonearm cable anti skate recommended by VPI plus the VTF is on the high side of the Dyn recommendation (2.2 gram). I did compare the alignment between the Mint Tractor and the VPI jig and the overhang is a couple of millimeters longer with the Mint Tractor. Zenith was close between the two but again slightly different. I can't say that alignment is the issue the OP is having but after using the devise correctly you become pretty confident that the system is dead on. But more importantly it sounds great.
Based on what you are hearing I find it hard to believe that there isn't something amiss with your system or set up, like alignment for example versus just not having the "ear" for analog. I've been digital most of my life and when I go from vinyl back to digital I can't help but get the feeling that digital (though more detailed in my system) is made up of a bunch of pieces and parts versus the flow of analog on my rather modest table. Good luck.
Based on what you are hearing I find it hard to believe that there isn't something amiss with your system or set up, like alignment for example versus just not having the "ear" for analog. I've been digital most of my life and when I go from vinyl back to digital I can't help but get the feeling that digital (though more detailed in my system) is made up of a bunch of pieces and parts versus the flow of analog on my rather modest table. Good luck.