Due to a not-given compatibility with Makerbot mechanical endstop wiring (and carelessness on my side) I ended up burning the voltage regulator on my Arduino Mega 2560. Now, powering the Arduino separately from a USB power supply, I can operate the electronics, however, I am still unable to receive any signal from the endstops and I don't want to hook up my replacement Arduino until I see that my wiring is correct.
Could I have burnt anything else on either the Arduino (pullup resistors were firmware disabled) or the RAMPS 1.4 which makes it impossible to receive a singal from the endstops?
Take a look at Ryan's answer to my question. I believe the MightBoard is based on the Mega 2560, so it is possible that some of the other components could have been damaged. If you look at the comments below Ryan's answer, we discussed the possibility of the processor itself being damaged. I had attempted this fix on two different MightBoards and they both ended up turning on, but the firmware wouldn't boot. So, it's safe to say that in my case, the processor on the Arduino was shot.
All and all, I'd recommend not using MakerBot's endstops as they seem to be the main culprit for this issue and has been for years (it happened to me twice since I got my machine in 2012).