If you have 115v on the secondary, you do not have a short in the secondary of the smps. It is probably clicking because the smps is in effectively an unloaded condition as the horizontal is not running.
Start at square one with the basics and work your way down from there:
- Standby voltage to system control and the 60Hz clock pulse from ac line.
- Turn on signal from system control, possibly both to relay and on I2C data bus.
- Horizontal run Vcc
- Horizontal drive pulses out of jungle ic
- Horizontal drive to the base of HOT
- Main B+ to the collector of HOT
- Then troubleshoot the reason for the shutdown, lower the B+ to the flyback system with a resistor or light bulb and scope the flyback waveforms.
- Then work back to the must have feedback signals, x-ray protect in line, h-sync return, v-sync return, I2C all ok return from misc ics, etc.