You can use this class to convert ItemStacks into Strings and Strings into ItemStacks.

ItemStackUtils

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.apache.commons.lang.StringUtils;
import org.bukkit.Material;
import org.bukkit.enchantments.Enchantment;
import org.bukkit.inventory.ItemStack;
import org.bukkit.inventory.meta.ItemMeta;
import org.bukkit.material.MaterialData;




public final  class ItemStackUtils {
		private static String getEnchants(ItemStack i){
			List<String> e = new ArrayList<String>();
			Map<Enchantment, Integer> en = new HashMap<Enchantment, Integer>();
			for(Enchantment t : en.keySet()) {
				e.add(t.getName() + ":" +en.get(t));
			}
			return StringUtils.join(e, ",");
		}
		public static String deserialize (ItemStack i){
		  String[] parts = new String[6];
		  parts[0] = i.getType().name();
		  parts [1] = Integer.toString(i.getAmount());
		  parts [2] = String.valueOf(i.getDurability());
		  parts [3] = i.getItemMeta().getDisplayName();
		  parts [4] = String.valueOf (i.getData().getData());
		  parts [5] = getEnchants(i);
		  return StringUtils.join(parts, ";");

		}
		public ItemStack deserial(String p){
		
		String[] a = p.split(";");
		ItemStack i = new ItemStack(Material.getMaterial(a[0]), Integer.parseInt (a [1]));
		i.setDurability((short) Integer.parseInt(a [2]));
		ItemMeta meta = i.getItemMeta(); 
		meta.setDisplayName(a[3]);
		i.setItemMeta(meta);
		MaterialData data = i.getData();
		data.setData ((byte) Integer.parseInt (a[4]));
		i.setData(data);
		String[] parts = a[5].split(",");
		for(String s : parts) {
			String label = s.split(":")[0];
			String amplifier = s.split(":")[1];
			Enchantment type = Enchantment.getByName(label);
			if(type == null) {
				continue;
			}
			int f;
			try {
				f = Integer.parseInt(amplifier);
			}catch(Exception ex) {
				continue;
			}
			i.addEnchantment(type, f); 
			
		}
		return i;
		}
		
}

Hacked at it a bit and it seems to work fine now: http://pastebin.com/1W4Esu7G

Until the deprecated methods are removed fully anyway.