I suspect your main problem was probably a failing U7 tube. And now you've got a new 5Y3 installed, too. What you experience is normal. The reason is that the Sovtek 5Y3 is not directly heated, as the NOS are. This makes a big difference in warmup time - or the delay before B+ arrives and the LED turns green.
Short warmup is ok with these preamp tubes under these low current conditions (do not try the same thing with power tubes, as they can experience cathode stripping over time). That's why I could get away with specifying the 5Y3 rectifier. I can also use a higher than data sheet input capacitor because the real story is about peak currents and energy ratings. Both of which I stay far within limits. Not to mention thos extra 220 ohm anode resistors you don't see on other equipment.
Anyway, all voltages and hum will stabilize at about 30 to 60 seconds. After this first minute, the unit should be dead quiet. If it is making noise, we'll have a problem to talk about. If you don't like the start-up hum, then try switching to a GZ34 or something. Many octal rectifiers will work in this plug. It's a good way to try and see what you prefer for sonics.
jh