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North Star Horizon power

No problem. If it was simple, everyone would be doing it and there would be no reason for us to be here...

The short circuit between the +/-16V rails would certainly have driven the switched mode power supplies daft! It was a good job they have overload protection! You could have done some real damage there...

R32 reading 0.4 Ohms instead of 330 Ohms is (more than likely) a red herring I am afraid. All it probably indicates is a short circuit elsewhere between -16V and GND. Keep looking - you have done an excellent job so far and you are close to the finish line to getting this beast running again...

I suspect - with the short circuit between the +/- 16V rails - you may have inadvertently reverse-biased some of those tantalum bead capacitors. If (say) the -15V supply shutdown, this could put +15V across some of the capacitors (relative to GND) that are on the -16V line. My recommendation would be to recheck the pesky capacitors again. I am also not sure what this would do to the voltage regulators either.

Dave
You and Dwight were correct. I pulled the 79L12 and checked it by itself; with -12V on the input, I was only getting about -5V on the output. I pulled C1 and C2, and they were both bad. I replaced all those and found no shorts on the -12V rail. I powered everything up and all three power rails are working properly. The Vcc and -Vcc on the 1488 ICs are now reading correctly, there is +5V and +12V to the disk drive power connectors, and card connector pin 52 is now reading -16V. Everything looks good at this point.

Now I'll have to troubleshoot the cards. I'm hoping the Compupro CPU-Z and RAM-17 are okay. They only use the +8V rail. The Morrow Designs DJ/DMA fdc uses all three rails, so there is the possibility of problems there
 
Great news, well done!

It’s good when a plan comes together!

So getting annoyed with the power supplies and buying another switch mode supply would not have helped.

If you had the linear supply connected, I could see some more PCB damage could have occurred as a result of the short circuit(s).

Onwards and upwards...

Dave
 
Traces don't go away unless there's an over current event. I agree that there's still a short on the minus side. Easy test to so pull up one leg of the 330 ohm resistor if you want 100% proof. Reversed voltage tantalum cap's don't always go bang and let the magic smoke out, sometimes they just short out. I also notice that the positive power must be connected to ground somewhere since you measured millivolts to ground. Make 100% sure that the general purpose supply you are using as the negative supply isn't connected to ground with its negative lead. This lead has to be used as -16 volts for the motherboard. If it is tied to ground then you will short that supply.
 
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