It’s been along time since my last update, but I’ve managed to measure the magnetron spectrum output using a Signalhound. I sent an email to Signalhound and this was their reply:
For quick hoppers (FHSS), you will probably need to turn image rejection off to catch the signal. This will speed up the sweep but will also pass the image frequency (21.4 MHz below frequency of interest). If you turn video bandwidth down to 6.5 KHz and RBW to 25 KHz, Power Average mode, then turn on Max Hold, you should be able to capture and measure the signal.
These suggestions pointed me in the right direction to get the Signalhound working the way I wanted. Unfortunately I think the signal is very rapidly changing frequency so the max hold suggestion is the only way to see the signal.