I built this Programmable TARDIS and recently finished the materialization system. I imagine it would be extermely difficult to figure out how to program in the destinations without a comprehensive guide, so that's what this is. Some understanding of command blocks is ideal, but if you follow these instructions carefully you should be fine. General warnings are don't destroy blocks, especially not redstone stuff or command blocks, and don't edit commands unless you really know what you're doing.

INITIAL SETUP
The most important part of placing the TARDIS schematic in your world is that you put it in exactly the right place. The commands I used assume that the TARDIS is centered at 0,0,0 so if you're off by even one block nothing is going to work correctly.
1 - load up the world you want to place the TARDIS in and switch to creative mode
2 - travel to the 0 coordinate of the x and z axes and dig a 1-block column straight down
3 - destroy all of the blocks (including bedrock) within a few blocks of the origin, so that you are floating over the void in a small empty room
4 - use the command [ /setblock 0 1 0 glowstone ] to place a block of glowstone as a marker
5 - close minecraft, open MCedit, load the world you were working on
6 - Import the TARDIS schematic and click somewhere in your empty room to place it in roughly the right place
7 - use Nudge to move the schematic so that the small bedrock indicator towers are one block higher than the glowstone on each side, then hit the Import button
8 - Save the world, close MCedit, and go back into your minecraft world
9 - Swim up the waterfall into the first room, and hit the reset button there
10 - Wait at least one minute, then hit the reset button again. In the future you will only need to hit the reset button once, but the initial startup is a bit harder.
11 - If the lights flash, the world goes wibbly-wobbly, and you get a ton of command block messages in the chat, then congrats! you have placed the TARDIS in the right place! Use [ /gamerule commandBlockOutput false ] to stop those annoying status messages in the chat and you're ready to move on. If not, go back to the beginning and try again, sorry :/
12 - Once you get the TARDIS box itself in the right place, you may want to consider adding this barrier around the beacon so no one can get in simply by breaking a few glass blocks. The barrier has the added bonus of making the respawn mechanic work correctly. Just open up MCedit, line it up with the glass block in the center of the TARDIS box, and import it with the "Copy Air" box unchecked so you don't destroy whatever landforms were conveniently covering the top of the TARDIS Interior.

SETTING A DESTINATION
This part is just a bit trickier. Nothing too difficult, but it can get fairly tedious and it is maddeningly easy to run into off-by-one errors (which in this case can mean materializing halfway into the side of a building). Follow along carefully though and you should be fine.
1 - Outline your desired landing space.
2 - Stand in the center of your marked landing space, facing the direction you want the door to be. Use F3 to record your coordinates and the direction you are facing.
3 - Choose a destination number you would like to tie to this location. Note that destination 0 is only used by the reset button, and locations 3, 10,11, 19, 20, 22, and 23 are private locations only accessable under special circumstances.
4 - The left side row of command blocks (the one with no redstone leading to it, that has a purple repeat command block at its beginning) has signs on the granite below indicating what each command block is supposed to do. Command blocks without signs are not meant to be edited.
5 - Copy the following commands into each command block. Replace x, y, and z variables with the appropriate coordinate from your landing location, and when a command includes a variable in parentheses replace that entire segment with the result of the operation in the parentheses. For example if you see (x-1) in a command and your landing location has an x-coordinate of 138, you would type 137 where the parentheses were. Some commands depend on your facing, in which case a slightly different command is listed for each direction. Make sure you select the right one.
6 - Almost done, now move to the short row of command blocks at the end and copy in these commands just like in step 5.
7 - Return to the Console Room, set your destination, and activate the Materialization Circuit. If you copied everything in correctly you should now be able to walk outside to a new place!

OPTIONAL SETTINGS