Cross-posted from the MOUL forums, because I came up with it off the top of my head and I think it works as a general answer to the general question. YMMV, but this is my view.
How does a fan make an Age?
Start with a story. The world you're going to create was made (Written) deliberately, which means it was made for a reason and a purpose. What was that reason, and that purpose? Did the Age do what it was supposed to, or did it surprise its Writer? Invent the Writer, either yourself (which doesn't take much inventing) or some long-ago D'ni person. Why did s/he Write this Age in particular? For a place to read in peace? Because s/he thought a pink sun would look nifty? As a source of troops to wage a war, or a place to get that particular kind of spice which adds such zing to a curry?
Get those questions settled, and you'll be starting to have an idea of the general shape and look of your Age. Now sit down with some paper and a pen or pencil and plan. Make your maps, draw out your machines if any, build your puzzles, work out exactly what you want to happen where and when. Try not to make it too linear. Explorers don't like to be herded from A to B to C; they like to be able to look at F or K on the way from C back to B. You have a story you want to tell with this Age, but there's no harm in keeping it a little loose, allowing for the player's whim. (Plus you may have better ideas along the way. That's always a good part.)
When you've got your plan all set in your head, write the journals or whatever that are going to give your players the backstory of your Age. Bear in mind that people don't like to read more than a couple of pages at a time (I know, weird, isn't it?) so keep it succinct. Make any art you want in there; compose (or get a friend to compose) the music and the soundscapes. Your aim is to get this Age so completely worked out that if you were to fall into a coma from sheer exhaustion, someone else could come along and make it from your notes. That's the best way to be sure you've got it right. No sense uploading an Age unless and until you're absolutely sure you've got rid of most of the silly mistakes.
And then, when you've done all that...then you go to your computer and you fire up (yech) Blender, or Max if you happen to be lucky enough to have it, and I refer you to my distinguished colleagues.