Have X & Z movement working in a space RTS...how about Y?

Hi all, fairly new to unity still figuring things out, have a lot to learn on the programming side.

Anyway what im trying to do is something similar to the old Homeworld games, but with waypoints. Ie you have a main mother ship click on it to select it, click where you want to move it in terms of X & Z axis then once you have clicked be able to set the Z value and then have the ship accelerate and then decelerate to that position.

Now the following script i found from the Unity Community wiki it is as follows.

 /* 
  * Esse Script movimenta o GameObject quando você clica ou
  * mantém o botão esquerdo do mouse apertado.
  * 
  * Para usá-lo, adicione esse script ao gameObject que você quer mover
  * seja o Player ou outro
  * 
  * Autor: Vinicius Rezendrix - Brasil
  * Data: 11/08/2012
  * 
  * This script moves the GameObeject when you
  * click or click and hold the LeftMouseButton
  * 
  * Simply attach it to the gameObject you wanna move (player or not)
  * 
  * Autor: Vinicius Rezendrix - Brazil
  * Data: 11/08/2012 
  *
  */
  
 using UnityEngine;
 using System.Collections;
  
 public class moveOnMouseClick : MonoBehaviour {
     private Transform myTransform;                // this transform
     private Vector3 destinationPosition;        // The destination Point
     private float destinationDistance;            // The distance between myTransform and destinationPosition
  
     public float moveSpeed;                        // The Speed the character will move
  
  
  
     void Start () {
         myTransform = transform;                            // sets myTransform to this GameObject.transform
         destinationPosition = myTransform.position;            // prevents myTransform reset
     }
  
     void Update () {
  
         // keep track of the distance between this gameObject and destinationPosition
         destinationDistance = Vector3.Distance(destinationPosition, myTransform.position);
  
         if(destinationDistance < .5f){        // To prevent shakin behavior when near destination
             moveSpeed = 0;
         }
         else if(destinationDistance > .5f){            // To Reset Speed to default
             moveSpeed = 3;
         }
  
  
         // Moves the Player if the Left Mouse Button was clicked
         if (Input.GetMouseButtonDown(0)&& GUIUtility.hotControl ==0) {
  
             Plane playerPlane = new Plane(Vector3.up, myTransform.position);
             Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);
             float hitdist = 0.0f;
  
             if (playerPlane.Raycast(ray, out hitdist)) {
                 Vector3 targetPoint = ray.GetPoint(hitdist);
                 destinationPosition = ray.GetPoint(hitdist);
                 Quaternion targetRotation = Quaternion.LookRotation(targetPoint - transform.position);
                 myTransform.rotation = targetRotation;
             }
         }
  
         // Moves the player if the mouse button is hold down
         else if (Input.GetMouseButton(0)&& GUIUtility.hotControl ==0) {
  
             Plane playerPlane = new Plane(Vector3.up, myTransform.position);
             Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);
             float hitdist = 0.0f;
  
             if (playerPlane.Raycast(ray, out hitdist)) {
                 Vector3 targetPoint = ray.GetPoint(hitdist);
                 destinationPosition = ray.GetPoint(hitdist);
                 Quaternion targetRotation = Quaternion.LookRotation(targetPoint - transform.position);
                 myTransform.rotation = targetRotation;
             }
         //    myTransform.position = Vector3.MoveTowards(myTransform.position, destinationPosition, moveSpeed * Time.deltaTime);
         }
  
         // To prevent code from running if not needed
         if(destinationDistance > .5f){
             myTransform.position = Vector3.MoveTowards(myTransform.position, destinationPosition, moveSpeed * Time.deltaTime);
         }
     }
 }

Now this works great for moving in the X & Z... and i think i roughly understand what its doing... (one issue is it rotates really quickly so i need to put something in for that, plus acceleration and deceleration.)

So my idea for adding what i need is to somehow turn the first ray check into just a pause of some sort and it gets the value of the x and z position, then create another plane from that position aligned to the y axis then you can move the mouse up and down and get the y value and move to that position in space...right?

So am i on the right track and any idea where i would start to do this?