(Resolved) Continue running one part of code while still checking other inputs?

He's right. And as to why it ignores the switch:

int BrakeSwitchMillis = 0; //Time stamp for when the switch last went to 1(HIGH). Initially set at 0(LOW)

...

  BrakeSwitchVal = digitalRead(BrakeSwitch); //read and store brake switch status
  if ((BrakeSwitchVal == HIGH) && (previousBrakeSwitchVal == LOW)) //compares current switch status to previous status
    previousBrakeSwitchVal = BrakeSwitchVal; //sets the current status as the old status in preparation for the next check
  BrakeSwitchMillis = currentMillis; //sets a time stamp at the current time

That last line is done unconditionally (despite your indentation). If it is supposed to be when you press the switch that is not what you are achieving.

You need the squiggly brackets:

 BrakeSwitchVal = digitalRead(BrakeSwitch); //read and store brake switch status
  if ((BrakeSwitchVal == HIGH) && (previousBrakeSwitchVal == LOW)) //compares current switch status to previous status
    {
    previousBrakeSwitchVal = BrakeSwitchVal; //sets the current status as the old status in preparation for the next check
    BrakeSwitchMillis = currentMillis; //sets a time stamp at the current time
    }