How can I get a character to patrol and follow terrain?

I've seen many forum posts and answers related to parts of this question, but I can't seem to get it to work together properly. I have a character that I want to patrol waypoints and follow the terrain while doing so. I have patrolling waypoints working, but really only if the Y value of each waypoint is the same. My thought is to have the AI patrol the waypoints based only on the x-z plane and ignore the y value, and use raycasting during update to keep it on and aligned with the terrain. Not sure what to do really.

Here's what I have so far:

 using UnityEngine;
 using System.Collections;
 
 public class PatrolWaypoints : MonoBehaviour {
     public Transform[] waypoints;        // The amount of Waypoint you want
     public float patrolSpeed = 3;        // The walking speed between Waypoints
     public bool loop = true;            // Do you want to keep repeating the Waypoints
     public Transform player;            // Referance to the Player
     public float dampingLook = 6.0f;    // How slowly to turn
     public float pauseDuration = 0;        // How long to pause at a Waypoint
     
     private float curTime;
     private int currentWaypoint = 0;
     private CharacterController controller;
     
     
     
     void Awake() {
         
     }
     
     void Start() {
         controller = GetComponent<CharacterController>();
     }
     
     void Update() {
         RaycastHit hit;
         if (Physics.Raycast(transform.position, -transform.up, out hit)){
             transform.position = new Vector3(transform.position.x, hit.point.y, transform.position.z);
             transform.up = hit.normal;
         }
         
         if (currentWaypoint < waypoints.Length) {
             Patrol();
         } else {
             if (loop) {
                 currentWaypoint = 0;
             }
         }
     }
     
     void Patrol() {
         Vector3 target = waypoints[currentWaypoint].position;
         //target.y = transform.position.y;                        // Keep waypoint at character's height
         Vector3 moveDirection = target - transform.position;
 
         if(moveDirection.magnitude < 0.5) {                        // If this number is 1 the character will jerk the last bit to the waypoint and not be over it
                                                                 // any lower and the character will get stuck for a second over the waypoint on the iPhone
             if (curTime == 0) {
                 curTime = Time.time;                            // Pause over the Waypoint
             }
             if ((Time.time - curTime) >= pauseDuration){
                 currentWaypoint++;
                 curTime = 0;
             }
         } else {        
             //transform.LookAt(target); // Use this instead of below to look at target without damping the rotation
             // Look at and dampen the rotation
             Quaternion rotation = Quaternion.LookRotation(target - transform.position);
             transform.rotation = Quaternion.Lerp(transform.rotation, rotation, Time.deltaTime * dampingLook);
             controller.Move(moveDirection.normalized * patrolSpeed * Time.deltaTime);
         }
     }
 }