we’ll just go ahead and remove the onboard rectifiers
That sounds like making random changes without any theory of operation to test. If you do that at the same time as moving the transformer mounting location that is two simultaneous changes without any way to distinguish which (if either) made a difference.
To track down problems like this you have to both be systematic in testing, and have a grasp of fundamentals of current flow to understand (at least somewhat) the effects you see to know what a reasonable next step would be.
Here is what I would do to try to track down this problem.
1. Remove the spaghetti mess of connections from the different PCBs to the chassis. There should be 1 connection from the power supply return to the chassis, ideally right at the filter cap(s). The PCB does not appear to have an easy connection point there, so don't sweat exactly where it connects.
Since there are separated power supplies for each buffer PCB that really means one connection from each SRPP board.
I cannot see the connections on the bottom side of the PCB, making only one connection to chassis may involve using insulated stand-offs if the circuit gnd node surrounds the mounting holes.
Connect the cable shields on input and output connectors directly to the chassis and only there.
2. Assuming that did not solve the noise problem, measure the noise voltage at the output (i.e. between pins 2 and 3 of an output connector), then disconnect the powered monitors and check the noise voltage again. That is making the assumption that the voltage is high enough and your voltmeter is sensitive enough to easily see if the noise is present just from the AC voltage measurement.
If removing the connection to the monitors gets rid of the noise then figure out where the rule about cable shields connect only to chassis was broken and fix that. If the problem is in the monitors (i.e. the monitors have a pin 1 problem) then most likely you will be able to hear the problem, but not measure it at the output pins. You might be able to bandage your monitors with a modified cable if that is the case.
3. Assuming disconnecting the monitors did not solve the noise problem, strip the problem back to the most basic configuration possible.
You cannot have an output without the SRPP boards, so disconnect everything except power to the SRPP boards and pins 2 and 3 on the output connectors to the SRPP boards.
The diagnosis splits at this point. If the noise it not present, then start connecting pieces back one at a time, one connection at a time. So connect a twisted pair from the output of one EQ board to the input of the buffer board and check the noise. Connect the second buffer board and check the noise, then connect a twisted pair from the secondary of the input transformer to the input of one EQ board and check the noise, etc.
If the noise is still present with the only connections being SRPP boards with power input, and the output connections to the output XLR connectors, you will really need to find a friend with an o'scope so you can see what is going on in the buffer circuits. That circuit is just about as simple as you can get for a tube buffer stage, just one step up from a cathode follower, with nothing connected on the input side there should only be a slight amount of white noise.
If there is still noise, power only board A (which you said was quiet before), then only board B (did you ever try only board B, or just A alone, then A+B together?), then A and B together again. Is the noise really the same from both boards, or just similar? Do the heater voltages change at either board between one powered or both powered? They are regulated, so should not change at all, should be 6.3V always.
How much does the HT voltage change at each board between each board powered singly then together? The HT voltages are not regulated, so I would expect the voltage to drop at least a little when both boards are powered compared to only one.
Is the voltage across the 1K cathode to plate resistor and the 470 ohm cathode resistor the same on both SRPP boards? They should be close if both tubes are operating properly.
Hopefully somewhere along that path a change makes enough improvement to give a clue what is going on.