What is crosstalk like on the direct outs? What does the rest of the grounding scheme look like?
I have a couple of these RCA 9 pin input transformers just waiting for me to build them a home. Its been a while since I looked at them, but I believe a lot of other brands used the same pinout or at least one that is compatible? Newcomb, Webster, Dukane, McMartin, etc. Could be fun to try different iron!
I don't understand why you're continuing to ignore Gyraf's expertise on NOT grounding the input, especially with the plug-in transformer that you've chosen. That MI-12399 has three taps on the primary, but those taps are for giving you multiple choices of impedance, not for grounding. It has its own shield ground, so any rare need for grounding the center tap is unnecessary with this transformer... leaving no good reason to use it. Here is some good news, though. That switch you've already got in there, NOW you can repurpose it to a useful function and rewire it to select from the two different impedances! Also, I can't be the first person to suggest your wiring is way, WAY too thick. And that tube circuit sub-board needs more support. You've got it dangling like a diving board! Uhhh....
Anyway, here is a similar Newcomb input, the TR-91. It has dual primaries that can potentially give you THREE different input impedances! For your circuit, you would just bridge pins 6 and 7, which won't effect your RCA iron.