Input.GetButtonDown("Fire1")

...will only return true once, when the key is first pressed.

Input.GetButton("Fire1") 

...will return true so long as the key is held down.

If that's returning you errors, you need to post them up.

EDIT: Here is an example that is tested and works (and if it doesn't, your issue is elsewhere):

public class BulletTest : MonoBehaviour
{
        public int iClipSize = 10;
        public float fReloadTime = 2;

        private float fReloadCount = 0;
        private int iBullets;
        private bool bReloading = false;

        // Use this for initialization
        void Start ()
        {
                iBullets = iClipSize;
        }

        // Update is called once per frame
        void Update ()
        {
                if(Input.GetKey(KeyCode.A))
                {
                        if(iBullets > 0)
                                Debug.Log("Bullets :" + --iBullets);
                }

                if(Input.GetKey(KeyCode.R))
                {                      
                        bReloading = true;
                }

                if(bReloading)
                        Reload();
        }

        void Reload()
        {
                fReloadCount += Time.deltaTime;

                if(fReloadCount > fReloadTime)
                {
                        Debug.Log("Reloading");
                        //yield return null;//new WaitForSeconds(fReloadTime);
                        Debug.Log("Reloaded!");
                        iBullets = iClipSize;
                        bReloading = false;
                        fReloadCount = 0;
                }
        }
}

This question was hard to answer because you mentioned GUI, so I thought you meant a GUI.Button.

Instead of Input.GetButtonDown("Fire1"), you should use Input.GetButton("Fire1"). That will return true as long as the button is held, instead of just the frame it's pressed.

Hope that helps.