I don't know of a way to turn them off directly, that's a SOC function. It would be easy to place tape over them and just cover them up.

You don't need to replace the NFC, but I'd replace the lower and upper if you're going to replace either of them. The Moto X depends on both antennas to meet their dual antenna MIMO spec. and it would be a waste of time to guess which one is borked up. Before you replace the antennas though, I'd suggest opening it up and just removing / reseating the antennas first. It could be as simple as one of their connections being loose and introducing interference into the circuit.

If you feel comfortable opening the device, disconnect it from the computer and remove the cover (you'll need to find instructions on this!) Then take a liberal amount of isopropyl alcohol (90%+) on a Q-tip and clean the port and connector area, allowing it to dry. You likely have some sort of deposit or short forming near that connector where the water ended up. When cleaning it look for material bridging some of the connectors and gently wipe any away that you find. After you give it time to dry (20 minutes is fine normally) try it using it again.

If a power spike damaged the system I don't believe anyone can honestly tell you the exact part that needs replacement. The question is how many items on your board need replacement to fix it. If you don't have experience fixing motherboards and soldering you will likely require assistance for repairing this device.

Send the unit back as a defective unit. If it's brand new, you shouldn't be having to fix it.

Reinstall your graphics drivers and see if that fixes the problem.

Can you include an image of the chip and the location it came from?

Did you try plugging it into a charger and testing the button again?

If it runs for a while and then starts doing this, it's likely overheating. Modern systems have a thermal safety where the processor itself will deactivate above a safe level. Check the vents and clean them out with canned air. If that isn't the case, first disconnect any and all external devices (including USB nubs, etc) and try powering it back on. If that doesn't fix the problem, try removing all but one RAM stick and removing the hard drive and CD/DVD ROM. Try turning it on then. If that still doesn't work, remove ALL the RAM and check for a beep code. If you get one, you know the motherboard is at least still working enough to give a no-RAM code. Try alternating the RAM sticks to see if it works.

This doesn't sound like a video card issue, it sounds like a short circuit somewhere (maybe a blown cap or resistor? no way to tell without inspecting). Shutting down when you open the lid would indicate to me a safety mechanism when the unit detects a short or power spike trying to engage the primary display, and one of the involved chipsets terminates the power to avoid permanent damage. I don't believe it's a loose connector, because that isn't normally so predictable a result.