Edit: He has an older GA40, with a different tube line up.How are you numbering these tubes?
It should go, 1/2 = preamp 5879, 3 = LFO 6SN7, 4 = PI 12AX7, 5/6 = 6V6 Power tubes, 7 = 5Y3 rectifier tube. If that's the way your numbering them, then with V7 the rectifier tube pulled, you will have no dcv, so no other tubes will turn on, so no noise. 5. V4 removed. No startup noise.
6 Added back V4. - Startup noise is back. This is the Phase inverter/tremolo. It’s a 6SN7 tube.
No, 12AX7 is the PI tube, the 6SN7 is the trem LFO (low frequency oscillator) tube. Counting forwards from 5879 or backwards from 5Y3 it's still V4.
Try a different 12AX7. It could be a dirty tube socket, the tube, or a bad tube plate R.
Have you cleaned the tube socket and re-tension'd it?
That's an old amp, you should clean and re-tension the all tube sockets.
After you get V4/
12AX7/PI fixed, I'd still do this too;
Start with all the tubes in. With amp off, pull V1, turn amp back on, listen, then turn off amp, pull V2, turn amp back on, listen, turn amp off, pull V3, turn amp back on listen.
If 1 pulled tubes quiets the amp, then work backwards, start with V3, to find which tube section is the problem. Turn off amp, pull V3, listen. Then turn off amp, put V3 back in, pull V2, listen, etc..... It might be more than 1, even all of them.
Plate R's from the mid 50's were cracked carbon. They actually develop cracks in them from years of going through the heat/cooling cycle of the amp being played, heating up, then being off. Because of this they absorb moisture over the years and hiss and pop.