No reason to mod the motherboard, so let's leave that untouched. Could you check the resistance from REGE to Y? I'm expecting it to be around 0 ohms. If you can, remove that 0 ohm link shown in the last picture and recheck the resistance from REGE to Y. After removing the link It should be disconnected which means there's no worry about the motherboard any more. At that point any means of shorting Y to GND should be safe, so either try using the 0 ohm link you will have just removed, or if you have a conductive pen you can use that.
On removing SMD components, don't apply force to lift them, you might damage traces and vias. Depending on the size of the soldering iron tip then you may be able to melt both ends at the same time, then use a pair of small tweezers to just lift it up.
The other option would be to find the 10k pull up resistor, remove it and put it between Y and GND. Not sure where it is. You'll be looking for a single resistor marked 103. I'm guessing it's one of the ones on the top, so measure the resistance between pin 28 on one of the registers and the various resistor pads. Eventually you should find one that reads close to 0 ohms. The other side of the resistor should be connected to Vcc. If you can find that, then you've found the pull up resistor.