To answer some questions above.
boeingpilot (supercool nick!), attaching shorting plugs did not help and obviously my turntable ground is attached to PAS chassis. It is definitely picking up noise inside the preamp.
rjpjnk, I do understand what you're saying, and I experience it with many phonos in my house. At full volume, I am measuring 20-25mV peak to peak noise on phono background.
tubes4hifi, I did remove two phono wires (L/R) from the rat's nest, tightly twisted them in a separate run. It didn't help. I did disconnect phono grounds jumpers from other grounds on the back panel, so like you said, phono input grounds were only connected to dedicated black wires going to phono board.
I also followed my Regenesis power supply manual suggestion, and rerouted two bottom ground wires from phono board, which ran to the stacked capacitor, closer to the new power supply board - to the bolt that holds that board. This actually helped a little bit.
I used to hear this noise at 1 o'clock on the original volume control pot, or at about the same level on new Alps pot. After I removed loudness contour completely, volume control is now much more linear. It is definitely louder at around 11-12 o'clock, and that's where I like to listen with my system. Background noise starts at around 12 o'clock now.
Oh, I never understood why phono inputs go to the selector first. Next time I'll be opening this preamp, I will follow your suggestion and will move the input wires and RIAA capacitors to the phono board. There is only so much I can squeeze out of this amp with original boards/circuits.