Tung sol, EH and Mullard 12AX7 would give me the hum when used in V3 and V4. With Mesa branded JJ tubes, I would get white noise (hiss). It was apparent in CH1 and CH3, CH2 would be whisper quiet. However, the noise is not intermittent (generally but it could be).
How old is the Rectifier tube? It can create noise even if you are running 90W since it is never turned off and is always in the circuit. It is possible that one of the rectifier circuits of the tube are intermittent. If the tube is good, just remove it and reinstall it (could be poor contact). The noise is definitely DC supply related and the noise is generally a form of excess ripple (if the Rectifier tube is bad or partly bad it will cause noise, the fuse will blow only if the tube creates a short).
It could also be a bad instrument cable or internal to the guitar (that one is easy to rule out).
The last thought, since the top of the amp is lined with foil, depending on how many times you have removed the amp chassis from the shell (if at all), the foil heat shield may become scratched or damaged and is probable there are small pieces of the foil on the circuit board of the preamp. Also if you have ever done tube rolling with the amp out of the chassis, the tube shields do shed metal fragments from removal. Remove all the shields and tubes and look inside at the surrounding tube sockets for metal dust. If it is there, high pressure air can be used to remove the metal dust. If that is not available, I have also used a Q-tip soaked in isopropyl alcohol or acetone to clean as much of the debris off the circuit board (clean the rubber o ring on the tube shield too).