I think I'm going to get some replacement transistors for the small boards. At the moment one of the boards works but still causes buzzing and the other board's LEDs will not light up (tried fresh LEDs as well, so it's not them, and tried the board in both channels), nor will the corresponding LED in the 9 pin socket. I've resoldered all the wires and capacitors around the transformer and replaced and resoldered the wires that attach to the small PCBs. I figure that having the resistors switched at the start must have damaged the transistors on the small boards.
Also, the large board is currently installed, and with the 22.1k resistors, it works fine. The problems caused by the small boards occur whether the large PCB or the 3K resistors are installed, so I believe that the large PCB is functioning correctly.