After following the great fan installation at http://www.praxxus.com/cubefan I decided to document how I attached the Molex connector to my Cube fan. Although the actual installation was easy, the connectors were a bitch. You may not be lucky enought to find a Molex this size already assembled. I thought this may be out of the realm of a lot of people and wanted to help you guys out. So here it is.
Here is a list of everything you'll need.
1. Sharp pair of wire cutters.
2. Needle nose pliers
3. Extra fine rosen core solder
Radio Shack # 64-009
(the rosen helps the solder stick to everything)
4. Alligator clip holder
Radio Shack #64-2063
5. Low wattage Soldering Gun
Radio Shack #64-2070
(Higher wattage guns will be bulky and make a mess of everything. This is a delicate procedure and you need a delicate gun)
6. Wire strippers
(not shown)
7. And of course the fan, Molex crimps and housing
(Be sure to buy more than you need. They're cheap enough and you will make mistakes.)

You don't need everything I have here but having the right tools makes any job easier.
Step 1:

Cut wires short like so. Note the front, back, top and bottom of the crimp. You'll need to know this later on.
Step 2:

Add solder to tips of wire. Be careful not to melt insulation.

Don't try to solder the clip directly to the wire. You'll end up getting too much solder on the connections. Soldering the wire first makes sure you have just enough.
Step 3:

Insert crimp into the alligator clip so only the back of the crimp sticks out. (Only the last two "wings" of crimp should stick out.)

Snip wire again, long enough so the insulation of the wire touches the crimp.

The alligator clip will prevent any solder from seeping into the front of the crimp. (Be careful, if any solder does make its way to the front the connector it will not fit into the male connector on the board.)

Heat the body of the crimp to melt solder. Be careful not to melt the insulation. If you feel you need to add more solder at this point, be very careful not to add too much. The wires end up being very close together when assembled and you don't want them making contact with one another.
Step 4:

After soldering both crimp terminals, note how far the wire extends into the terminals. (If they extend too far the connector will not fit into the male connector on the board.)

Then carefully crimp the tips inward. Or cut them off entirely. (Careful, the terminals may be soldered but it doesn't mean they won't come off if you handle them too much.)
Step 5:

Now carefully push the wires into the housing. Using the needle nose pliers may help. If you did everything right the insulation will butt up against the housing ensuring the wires won't make contact with one another. The tops of the crimps should lock onto the housing as shown.

A dab from a hot glue gun will help secure the wires to the housing and also help ensure the wires never touch together should they come loose.

Be sure the red wire goes on the left and black to the right. The fan won't work if you mix them up.
The final product:

Your new Molex connector should fit into the male connector on the board firmly and snugly with a slight snap. If it does not you did something wrong. Also when installing the fan the silver sticker should face up. I'm sure you'd hate having to take you precious Cube apart again just to flip the fan over.

You won't actually need the wire to be this long but you may want to practice first before you cut the wire to the right size. If you mess up and cut the wires too short you'll be sorry.

Good Luck,
kDawg