OK, you have made progress.
The fact that there are no problems when you plug into the FX return suggests that the PA, PI and NFB systems are all OK.
The amp will not sound that quiet once the preamp is in and the guitar is plugged in and turned up.
What happened to the horrible wailing, moaning and farting sounds we were listening to a couple of days ago ?
I thought they maybe had the makings of the latest trend in modern music

I hope they stay away forever personally, I'm a bit old fashioned.
Noise ( normal hum and hiss) assessments are only realistic if the PPIMV is set to full volume.
When the guitar is NOT plugged in there should be a noticeable hum and hiss on the CLEAN channel when all controls are set to full throttle. What do I mean by "noticeable" , much louder than a cats purr-r-r-r-r-r-r-r-r, but nowhere near as loud as a cat's meow.
(That is the only way I can express it in somewhat realistic everyday terms)
The CLEAN channel should be basically inaudible when all controls are set to 2 o'clock with the guitar not plugged in.
Just to clarify, where is the PPIMV set during these recordings. I would suggest turning all you knobs to about 2-3 o'clock with the guitar plugged in but turned down to like 1/8 volume (so that it doesn't howl and feedback) and then adjusting the PPIMV to make sure it is stable at all settings. Then turn all controls to full and adjust PPIMV making sure there are no signs of moaning / motor boating. Moaning and Hissing are very different things. Moaning can be very high pitched and sound like hiss but it is very different, it has a definite note ( fixed pitch or pitch bending up and down) buried in it.
There should be no hint of oscillation (moaning / wailing sounds), and no put put putter fart motor boating at any gain settings really, but at everything on spinal tapping 11 some amps may never be absolutely stable.
All the noise I am hearing on those recordings is coming from the clean channel, they are just made worse by the extra gain when overdrive is engaged. I am not sure if they are terribly abnormal although they do sound a bit too load to me. Depends once again on where the PPIMV is set.
Could the wailing / motor boating have been due to the lack of 4.7k NFB resistor and we got side-tracked / knocked of our rails inadvertently chasing ghosts. Possibly.
What type of resistors are you using around the first valve.
Now that was very long winded wasn't it. The actual sound of the amp is GREAT. What loudspeaker are you using.
If you could do those assessments and get back to us it would be helpful. We all love to hear others play on the amps they build so record some more with PPIMV at full tilt. If it's anything like my D'Mars you may need to put earplugs in and warn / bribe the neighbours.
PS: Ken Fischer of Trainwreck fame had his reasons I'm sure.