Variable updated in method not recognized in Update

I'm a bit confused on how these scripts work together. To simplify  it, you're turning off the box collider of the object containing this script once something with the tag of "frutgtable" or "shugcarb"  correct? The scripts you posted seem to do that just fine after testing it, although it can be simplified like this:

    void OnTriggerEnter (Collider col)
    {
        if (col.CompareTag ("Frutgtable") || col.CompareTag ("ShugCarb")) {
            TurnBoxOff ();
            GetComponent<BoxCollider> ().enabled = false;
            Debug.Log ("Hit Food right");
        }
    }

I left "TurnBoxOff()"in the OnTriggerEnter, but if it's only being used to enable/disable the collider it can be removed. Since I don't have any of the other scripts referenced I can't test those. Since both the scripts posted are very similar, you could use one generic script for both objects instead of separate scripts. No need to use Update or even separate methods if all you're doing is enabling and disabling the collider. OnTriggerEnter can do everything you need. 

After taking a break over the weekend and coming back I realized you are right and that the script has multiple unnecessary parts. I changed the script on the right collision box to the following. 

public class VisionRight : MonoBehaviour
{

public int collidersOff = 0, rightEyeSeesFood;
public FirstBabyScript firstBabyScript;
public VisionLeft leftScript ;
public BoxCollider leftCollider;

private void Start()
{
firstBabyScript = firstBabyScript.GetComponent<FirstBabyScript>();
leftScript = leftScript.GetComponent<VisionLeft>();
leftCollider = leftCollider.GetComponent<BoxCollider>();
}

private void OnTriggerEnter(Collider col)
{
if (col.CompareTag("Frutgtable") || col.CompareTag("ShugCarb") )   {
TurnBoxOff();
Debug.Log("returned from TurnBoxOff");
firstBabyScript.StartFindFood();
Debug.Log("returned from find food");
}
} 

public void TurnBoxOff()
{
GetComponent<BoxCollider>().enabled = false;
leftCollider.enabled = false;
Debug.Log("Turned right box off");
}

public void TurnBoxOn()
{
GetComponent<BoxCollider>().enabled = true;
leftCollider.enabled = true;
Debug.Log("Turned right box on");
}

}

This successfully deactivates the collision boxes once OnTriggerEnter is entered. Now the problem I am having is that StartFindFood is called and within the StartFindFood method the FindFood coroutin is called but none of the code in that coroutine is executed. Not even the Debug.Log at the very top of the FindFood coroutine. Below is the relevant code from firstBabyScript which contains StartFindFood and FindFood.

public void StartFindFood()
{
Debug.Log("In start find food");
StartCoroutine("FindFood");
}
public IEnumerator FindFood()
{
Debug.Log("In FindFood");

if (elapsedTime > 0){
Debug.Log("FindFoodSkipped!");
yield break;
}
speed = 0;
rayLength = 15;
while (elapsedTime < 1){
elapsedTime += Time.deltaTime;
transform.position += transform.right * Time.deltaTime;
yield return null;
}
elapsedTime = 0;

hit = 90;

if (leftEye == 1){
hit = hit * -1;
}

leftEye = 0;

rotateAmount = new Vector3(0, transformObj.eulerAngles.y + hit, 0);
startRot = transform.rotation;
endRot = Quaternion.Euler(rotateAmount);


while (elapsedTime < 5){
elapsedTime += Time.deltaTime;
Debug.DrawRay(transform.position, transform.TransformDirection(Vector3.right) * rayLength, Color.red);
if(Physics.Raycast(transform.position, transform.TransformDirection(Vector3.right), rayLength, foodRayMask)){
didntFindFood = 0;
break;
}
transform.localRotation = Quaternion.Lerp(startRot, endRot, elapsedTime / 5);
yield return null;
}

elapsedTime = 0;
speed = 20;
if (didntFindFood == 1){
collisionBoxTimer = 300;
}

didntFindFood = 1;

}

I do get the Debug.Log messages saying "in start find food" and "returned from find food". Do you have any idea why it is that none of the code in FindFood is being executed? Thanks!

I just figured out the issue. When I was manually assigning scripts in the inspector panel I was doing it from the wrong location. So for leftScript I made a brand new empty, applied the script to it and then dropped that into the public script variable rather than dropping the actual box collider with the script that is on my prefabbed animal. 

eithman Great. I would look at your console (Window > Console) as it will usually through an error or warning when you're having these kinds of issues. You might've seen a console error showing up in red at the bottom left of the Unity editor.