Boy, 99% of the time this is a backwards cap or diode (the silver bands on the 1N5818's and 1N5820's can be tough to see)
There are three sets of wires leaving the power supply PCB.
1. Going to the IEC power inlet
2. Going to the FC-1
3. Going to pins 1/9 on the 9 pin socket
4. Feeding the PC-2/9 pi socket
One at a time, remove #2, turn the amp on, check the fuse, the remove #3, turn the amp on, check the fuse, then remove #4, turn the amp on, check the fuse.
If the amp does not blow a fuse when you've removed one of those connections, you will have narrowed down the symptoms properly.
On the STP issue you mentioned, the 6.3V winding has a center tap that is grounded, so you may get a few Ohms of resistance between 1 and 9 to ground, with the continuity beep. If the readings of pins 1 and 9 on the 9 pin socket are different, please report that to us.
-PB