If you're going to replace A15U1 (CA3094A) it would be worth checking the voltages around it, and the operation of the HVPS without it, before you install the new IC. This is just a precaution because the CA3094A is a scarce commodity.
I also suggest that you fix the +48V regulator before moving on to the HVPS.
Once you've got the +48V rail up and running, here are a few ideas for how to check the HVPS without the CA3094A present.
With the old CA3094A removed, and the scope powered up, the HVPS should not run - that is, no glowing neons and no ozone smell.
In this condition you can measure the voltages on the U1 pads. Measure the voltages with the multimeter negative lead connected to the circuit's 0V rail, the chassis symbol that connects to several components near U1: R24, R20, and various small capacitors. The voltages should be:
Pin 3: +14V to +16V
Pin 4: -14V to -16V
Pin 7: +14V to +16V
Pin 8: +14V to +16V
The other pins aren't important.
Next, you can try running up the converter without regulation. You'll need a 20k multi-turn trimpot such as
http://www.digikey.com/product-detail/en/64WR20KLF/987-1064-ND/2408642. You might also want to get a trimpot adjusting tool
http://www.digikey.com/product-detail/en/H-90/H90-ND/262571 which won't slip off the adjusting head - it makes it much easier to adjust a multi-turn trimpot.
Turn the trimpot fully anticlockwise until it starts to click. Measure resistance between the middle wire and the two end wires. One will read around 20 kilohms, and the other will read close to zero ohms. Bend the latter one away. Connect the other two wires into pins 8 and 6 of the CA3094A position.
Connect your multimeter on voltage range with the negative probe to the 0V rail (as before), and the positive probe to the junction of R23 and R37.
Leave the HV MULT wire disconnected.
Power up the scope and note the voltage on the multimeter. It should be between +10V and +16V.
Now gradually turn the trimpot clockwise. This will increase the bias to the HV OSC transistor and increase the energy going into the HV transformer, which will cause the HV output voltages to increase. Unfortunately, there's nowhere to safely measure the HV output voltage because it's too high, but the voltage shown on the multimeter should drop as you turn the trimpot clockwise.
Keep turning the trimpot clockwise until either you notice an ozone smell, or any neons start to flash or glow, or the voltage reaches 0V. If the voltage reaches 0V and remains fairly steady, the rest of the HVPS is probably OK and it's safe to install the CA3094A. If you notice ozone or neons, make a note of the voltage on the multimeter and post it here.