Greetings,
I had a unit in my shop about 10 years ago with what seems to be the exact same problem. Worked on it for well over a month and it drove me nuts. I also replaced or swapped everything at least twice, all tubes, all caps, many resistors, went through each of the multi deck switches several times re-soldering every connection in the entire unit and verifying every wire, took apart and cleaned the Davon attenuators, etc.; literally everything I could think of.
Well, it DID turn out to be the IT! What was interesting is that under DC bench test conditions, the IT tested fine. Trying to test it in circuit, the Fluke 8060a meter I was using put too much load on that high Z portion of the circuit and was completely confusing things (and me).
If you have a VTVM available, you may have better luck and may be able to see the overshoot occur. What was happening was an internal breakdown of the IT windings. There would be a dramatic overshoot, and then it would gradually recover till the next over threshold signal started.
I proved the cause by quickly jumping in a tube P-P output tx in place of the IT. I can't recall exactly what it was that I used and it wasn't close to the same spec, likely something from a 2 x 6L6 or 6V6 gtr amp. It worked well enough to absolutely prove the IT was the problem. If it would help, I can look back in my files and get you all the details.
I was able to order a very good replacement from Sowter. Getting the old core out of the can was another difficulty. A hot air gun, several hours and MUCH smoke till enough of the black tar goop melted to pull it out. I used bees wax to "pot" the new one in and also had to repaint the can.
Of interest is I had two units from the same client. He had purchased them "as is" untested and without tubes, so there was no prior history to go on. They had not been stored in a very good environment.
The first one I rebuilt came out great with no difficulty. The other one I refer to above. When they were both complete, testing showed no discernible difference between the unit with the factory IT and the Sowter replacement. The client was unable to hear or notice any significant differences between them and was very happy to get them back.
Good luck, I'm glad to go look up my notes if it would help you out. I know how frustrating that one was for me!
Regards, Jim