First of all, please forgive me for editing your post; I just added some extra paragraphs to make it a bit easier to read =)
Hm. I don't think we explain how the DFN-system/JS engine "work" anywhere, actually. Should probably do something about that. Heh. We've got the syntax usage and overview of the JS Engine on the docs page (
here's a shortcut), but nothing that explains the basics

I'll try though:
The DFNs are simply "definition-files" for UOX3 - i.e. their purpose is simply to define various properties and values for items, npcs, regions, etc. You want to add a new item (not a one-shot item, which you can add/edit ingame, but one you want to use regulary), you either copy & paste an item from one of the .dfn files in DFNDATA\ITEMS\, into a custom .dfn file in the same folder (or subfolder) or into an existing .dfn file. What you need to have in mind though is that all sections in these DFNs, be it items or NPCs or anything else, need to have their own unique section IDs. You cannot have two sections with section header [0x13FA] for instance. So if you add your own items, you can give them header ids like.. [bluelongsword] or [0x13FA-custom] or whatever, as long as it's a unique ID. If you do add your own custom items, like the wand you spoke of, then it won't automatically appear in the item-menu which you access by using 'ADD. You must in that case either add it to the menu yourself (ItemMenu.dfn holds the menu-structure, while ItemMenu.bulk.dfn holds the actual items you can add), or add it directly ingame using the
'ADD ITEM my-item-id command. Like 'ADD ITEM bluelongsword, for using an example mentioned above. Stuff like artifact rarity isn't supported in UOX3 yet, by the way.
The JS files are scripts with events which can trigger for whichever item/npc the scripts are attached to. These JavaScripts are all registered initially in
JS\jse_fileassociations.scp in the form of
SCRIPTID=path-to-script. These scriptids have to be unique. For instance, take the line in this file which says
131=skill/tailoring/scissors.js. Script ID 131, points to scissors.js, which handles all the functions a scissor should have, like cutting cloth to bandages, shearing sheep, etc. Then in
JS\jse_objectassociations.scp script 131 is assigned to all scissors through the lines
..where 0x0f9e and 0x0f9f are the item-IDs of the two scissor-objects available. There's also other ways of assigning JavaScripts to items, if you don't want ALL items of that item-ID to get the script (for instance if you have custom items which use the same item-ID as another item); You can either use the ingame command 'SETSCPTRIGGER # where # is the scriptID, or you can add an extra line to your custom item in the .dfns saying SCRIPT=# where # again is the scriptID.
The only site which contains downloadable scripts for UOX3 is currently this one, and are kept in the Script Vault forum. Hopefully this will be expanded as people write scripts and submit them. Basically you copy & paste the text of the script you want to use, save it as it's own .js file in your UOX3\JS\CUSTOM folder (or anywhere else under the JS\ folder, but more organized that way), add a scriptID in jse_fileassociations.scp, and assign the script to an item or character using either of hte methods mentioned above.
You can tweak many properties of item ingame using the 'TWEAK command, which gives you an ingame menu of things that can be changed on an item. To set up teleporters, as well as other stuff, check my UOX3 Guide at
http://homefree.sensewave.com/~s107293/uoxguide/.
The id=0x0f6c for say, a blue moongate, defines that it actually is a blue moongate you're dealing with. It's basically what tells UO which graphics it should display, and in our case it's a blue moongate. For a list of such graphic IDs, check out
InsideUO, a very nice program for this. Run it, click on the Artwork-section, find an object, click on it, and you'll see the item-id at the bottom of the InsideUO window, like this:
Model No. 26 (0x1A). I've highlighted the important part of that in yellow. That's the hex-id, which is used in the dfns to determine the graphics of any item.
If you're unable to move items after you put them down on the ground, make sure you're A) a character with GM privileges, and B) that you have ALLMOVE enabled. Do that by using the 'ALLMOVE ON command.
How exactly did you make the skillgain moongate? Check out section 2.09 of my UOX3 guide if you haven't already, called Advancement Objects. It deals with this subject.