Suggestion: Dont make quest items have specific names. I stupidly got rid of the special nexus with out completing the quest and thus have to restart (i have nei in cheat mode just in case i have to cheat in an item). though once you complete the quest you could ditch the item but then that kind of defeats the purpose of getting it in the first place. Also a minor thing to note is that it is very possible to get quest items from reward bags. I opened a greater bag and got 5 of the item needed to "unlock" the Lost in Time questline.
Instead of restarting you can just add a recipe in the minetweaker .js files that gives you the named item with some simple recipe. It might take little digging to find the item (NEI dump) and get the name right if it has any special formatting, but will surely be easier than starting over.
Edit: I think there's also an easier method using an ingame command to give a named item but I'm not sure.