A microphonic tube is certainly a possibility. Try taking the head off the cab, move it away to the full length of the speaker cable. Does this make it stop, or affect the noise? If so, that would point to microphonics. You can try to isolate which tube is responsible by swapping in known good ones, or even swapping tubes of the same type between positions.
If not, I'd suspect a bad power supply filter capacitor. Those caps prevent the audio signal from feeding back through the power supply to a high-gain stage earlier in the amp. This can cause all sorts of weird noises: sometimes it is very low frequency and it goes BUP-BUP-BUP, (often called "motorboating") while driving your speakers past their excursion limits; it can whistle or whoop (which sounds like your problem); it can even be ultrasonic. You called your amp a "skunkworks", weren't those made two or three decades ago? That's a typical time frame for caps to start to fail.
It could also be as simple as a bad connection. It happened while you were playing, vibration could have finally broken a cold solder joint or loosened a connector.
Bottom line, though: if you don't find a microphonic tube, and you're not experienced poking around live high voltage circuits, protect yourself and your amp by taking it to a good tech!