IMO failed outputs wont give you a low collector to GND resistance, more likely to be something physical like damaged mica. I like the idea of pulling the fuses when doing such measurements, to break the path through rectifier diodes and transformer secondary.
D701 at 16V is odd but is not in play for the -ve rail/resistance measurement
You could try measureing dc voltage at each TP1,2,3,4 to GND, this should rule out the outputs.
I'd be inclined to remove the outputs and connect any diode handy (1N4148, 1N400x,,,) between output b-e solder pads, alternatively pull the outputs then measure resistance between collect solder tabs and GND.