I think your general idea where the problem is (Yig Coil-Drivers) is correct. An unmodulated signal shouldn't look like it does on your screen. Which means either the coil-driver itself, or the control circuits for the driver are bad / horribly out of calibration. Have you tried adjusting any potentiometers or measured them? What do the control-voltages for the YIG look like?
Btw. How are the Supply-Voltages doing? Voltage ok? Excessive Ripple? If one Tantalum has gone bad, there's a chance others are causing problems as well.
Also with the Cal-Signal supposed to be -30dBm, it's quite a bit lower on your screen. With strong harmonics (don't know if they are supposed to be there). I'd suggest you build a simple diode-detector (if you don't have any equipment to measure the cal-signal) and measure the output-power. Doesn't have to be precise, just a rough estimate to see if the signal is in the right area.