Well, the entire output stage has new amplifiers, but this was not the problem. So, I've stopped shotgunning it and started tracing the signal path.
I performed the CW leveling procedure IQCON 7.4.4.4 and found that the output from that module was ~2dB low. That has been rectified, but that wasn't the issue, either. Note: The SMIQ03 will run without the IQMOD module installed ("Press SELECT to simulate hardware"), so that R495 can be accessed when the front panel is removed and rotated out of the way. I have my SMIQ on it's side, which seems to work the best for keeping things out of the way but still accessible.
I then traced down the signal from the input connector X247 (FIQFIL) [schematic page 17] toward the FAM3300 off-page arrow. I see the amplifiers doing their thing along the path, with a selected frequency of 450.1 MHz and +13dBm selected. My analog o-scope only goes up to 470MHz, but the levels seem reasonable until I hit the Pi-attenuator R966/R120/R113. On the C593 side of things, the signal looks great (1.070V or 4dBm, just what we expect). On the C343 side of the path, the signal drops to something very low, and doesn't look like the 450.1 MHz signal I was tracing. I found R966 to be 51 Ohms, R120/R113 to be 100.0 Ohms, and there was a C590 piggy-backed across R966 which seems to be 1pF. This does not agree with the 1084.9800.01 schematic, but my board has a .08 revision, so maybe that's ok. This would be a 8.5dB attenuator, without the effects of the capacitor, which would allow a high-frequency bypass path for better leveling, perhaps?
I went ahead and replaced R966, but no joy. I can only think that something with the D_SWITCH circuitry is effectively grounding out the signal.
Next, I plan to lift C343 and see if the problem persists, to better isolate the problem.