Arduino Mega 2560 Smoking Shortly After Power On

This is my first post on this forum, if I'm in the wrong section or if I can provide any more information please let me know!

I'm engaged in a DIY robotic arm project that got me introduced to Arduino.

Long story short, I was using my multimeter to test some pin voltages when around 30 seconds after hooking up my power supply to my Arduino Mega 2560, my board started smoking. I quickly turned off the power, but to my dismay, while the green LED was still lit up my computer could no longer communicate with the board (there were no ports available, whereas COM3 was before). In addition, the TX, RX, and L orange LEDS were lit up (not blinking, just lit up).

I am using this Arduino Mega 2560:

With this Ramps 1.4 Shield mounted on top:

With these stepper drivers for my project's motors:

And this power supply to power the board:

I am looking for some insight as to what went wrong, or other precautions I could have taken to prevent this. I believe my power supply is hooked up correctly. After some research I have come to the conclusion that my 8u2 USB chip may have fried, though I don't know what caused it. One thing that may have happened was I may have touched one end of the multimeter to THESE two pins accidentally when testing voltages:

This is the only thing I can think of that may have caused the previously mentioned chip to fry.

I am very new to Arduino and was following a less than complete guide on how to apply it to my project. Any and all help would be greatly appreciated, as I am not knowledgeable on what can cause this sort of issue.

ADDITIONAL IMAGES:

Setup:

Stacked Setup