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 the
1. Standby voltage to system control and the 60Hz clock pulse from ac
line.
2. Turn on signal from system control, possibly both to relay and on
I2C data bus.
3. Horizontal run Vcc
4. Horizontal drive pulses out of jungle ic
5. Horizontal drive to the base of HOT
6. Main B+ to the collector of HOT
7. 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.
8. 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.