Need some MS3 help

So yesterday I was attempting to get my fuel pump and fan relays working correctly. I hop on google and see everyone has them wired as ground switched relays....fuel pump relay goes just fine, works as it should when I wire it that way, but I made a bad mistake with the fan relay...I forgot I had it wired to Fidle, which as I understand it is a 12v output...but speeding along I didnt think to double check how I had it set up on output, so I go to test it and lose communication between MS and my laptop...chances are I shorted it through that connection because I didn't stop to think. Anyway, I now have no communication with MS and its no longer working. Opening up the case shows no obviously fried components or traces, so I need a best guess as to what circuit/component was damaged by shorting the Fidle circuit that would cause loss MS to stop working entirely, or at least the best way to go about diagnosing. I built it myself from a DIYautotune kit...but all that really means is I followed assembly instructions, so my knowledge is fairly limited. I will buy another one if needed, but I would really prefer to fix this one if possible....so what is the worst that can happen shorting the Fidle circuit? Fried daughterboard?

FIDLE is ground switched too; only the stepper outputs are 12 volts. FIrst check if you have 5 volts on pin 26 (VREF) with the ECU powered up.

In reply to MadScientistMatt :

Alright, so pulled the MS3 from the car and brought it inside, plugged in the stim, it shows only 0.15v at pin 26 and a little over 3v at pin 28, but if I unplug it from the stim and measure at pin28 on the stim it shows a full 12v. So I assume whatever happened ended up frying the power supply circuit at the least?

If you don't have a solid +5V reference on pin 26 then you may have blown one of the polyfuses for the +5V circuit.  F1 is for all the +5V on the board and F2 is just for the Vref on pin 26.  I'd check and fix that problem first.

If you have a good stim 12v but it gets dragged down once you plug the MS in its likely the D12 zener diode. You can verify it by lifting one end of it off the board and continue testing. F1/2 I have rarely seen go bad, and usually if they are bad you get no voltage, not a fractional amount.

We do repairs and can turn it in a few days if needed.

Check D19 as well. That one pops if you have 12 volts get into the 5 volt circuit.