How can i add a time limit to running?

I would add a runDuration float, a regenTime float, and use an Enumerator to be able to count the durations. I haven't had time to test this, but I did run my scene with the script involved and no errors or warnings. This might not work exactly as you wanted but this should get you to the point where you can get this idea to work. This is more of an edit of your code with the necessary additions that you can experiment with, hope this helps :)

 using UnityEngine;
 using System.Collections;
 
 [RequireComponent(typeof(AudioSource))]
 
 public class RunAndCrouch : MonoBehaviour 
 {
     public float walkSpeed = 7; // regular speed
     public float crchSpeed = 3; // crouching speed
     public float runSpeed = 20; // run speed
     public float runDuration = 5.0f;
     public float runRegenTime = 15.0f;
 
     private CharacterMotor chMotor;
     private Transform tr;
     private float dist; // distance to ground
 
     bool canRun = true;
     bool tryRun = false;
     
     public AudioClip outOfBreath;
 
     // Use this for initialization
     void Start () 
     {
         ///AUDIO
         if(!GetComponent<AudioSource>())
             gameObject.AddComponent<AudioSource>();
         audio.clip = (AudioClip)outOfBreath;
         audio.loop = false;
         audio.playOnAwake = false;
         ///
         StartCoroutine("CheckRunEnergy");
         chMotor =  GetComponent<CharacterMotor>();
         tr = transform;
         CharacterController ch = GetComponent<CharacterController>();
         dist = ch.height/2; // calculate distance to ground
     }
 
     // Update is called once per frame
     void FixedUpdate ()
     {
         print (canRun);
        float vScale = 1.0f;
         float speed = walkSpeed;
 
         if ((Input.GetKey("left shift") || Input.GetKey("right shift")) && chMotor.grounded)
         {
          tryRun = true;
          if(canRun)
                 speed = runSpeed;
          else if(!canRun)
           speed = walkSpeed;
         }
        else
          tryRun = false;
 
         if (Input.GetKey("c"))
         { // press C to crouch
             vScale = 0.5f;
             speed = crchSpeed; // slow down when crouching
         }
 
         chMotor.movement.maxForwardSpeed = speed; // set max speed
         float ultScale = tr.localScale.y; // crouch/stand up smoothly 
 
        Vector3 tmpScale = tr.localScale;
        Vector3 tmpPosition = tr.position;
 
        tmpScale.y = Mathf.Lerp(tr.localScale.y, vScale, 5 * Time.deltaTime);
        tr.localScale = tmpScale;
 
        tmpPosition.y += dist * (tr.localScale.y - ultScale); // fix vertical position       
        tr.position = tmpPosition;
     }
 
     IEnumerator CheckRunEnergy()
     {
        while(true)
        {
          if(tryRun)
          {
           while(canRun)
           {
               yield return new WaitForSeconds(runDuration);
               canRun = false;
               audio.PlayOneShot(outOfBreath, 1.0f);
           }
           while(!canRun)
           {
               yield return new WaitForSeconds(runRegenTime);
               canRun = true;
           }
          }
 
 
          yield return new WaitForEndOfFrame();
        }
     }
 }