Alas, some weeks ago my E4407 TG has developed the same symptoms: "Output Unlevel" at >2GHz at levels above -3dBm.
I already did extensive investigations and replaced all parts which were easy to source, even playing with the various attenuators to see whether there is any effect, but to no avail.
The only parts left are the mixer and the mystery 1BR MMIC which I couldn't identify.
However, I doubt the issue is in the 768MHz path since neither replacing MGA-6 with MGA-6A (more gain) nor changing the 5dB attenuator did change the symptoms.
I'd also rule out the LO amplifier with the two HMC311 - reducing the 10dB attenuation didn't show any effect.
Accordingly, my current conclusion is that it's probably the HMC129G8 mixer.
Unfortunately this part is obsolete and not easily available anywhere, so I'm planning to replace it with HMC129ALC4 and an adapter PCB.
During my work, I compiled a set of schematics in Kicad. There are surely still a few errors, especially in the control board, but I'll attach the current version anyway.
Additionally, I accidentially popped the cover off the mysterious black cylinder labelled 0410-2110 and take a picture. I bet that's a crystal oven.
Cheers, Jürgen