
OK! so here is the basic calibration process:
first: calibrate the projection. This means that you need to drag your mesh vertices around until they fill your desired projection area.

This is a test calibration, which is all skewed to make sure that it can handle when the camera and the projection are misaligned. In a 'real' situation you would stretch the mesh to cover your entire usable surface.
In the mesh views, if you hold down the shift key, then you get some handles that allow you to scale and rotate all the vertices together. (shown in the first shot at the top) otherwise you just drag them around one at a time.
After you get your projection mesh set up the way you want (takes about 30 seconds), you leave the projection mesh up on the surface, and switch to the camera view. I took my visible light filter off so that i could see the mesh in the camera view:

notice that the mesh is 'keyed' with a circle at one corner and a square opposing it. this is so that you can make sure that everything is facing the right direction. In this case i just need to flip it horizontally (with the handy button for just that purpose)
Now just like in the projection mesh, you drag, rotate, and scale the mesh until it is close to the right size, then you manually move the vertices into position: (make sure the keys are right!)

almost there....

a finished mesh calibration. start to finish: about 3 minutes.
Just in case it is inconvenient to get to your camera and filter, you can easily do this a bit more manually with some printer paper and a sharpie:

a couple of sheets will do it... just lay them on the projection mesh and mark the vertices with a big black marker (but dont use one that will bleed through) alternatively you can just put stuff on your surface, coins, or toothpicks, or anything that will show up.

Be sure you can see the 'keys'..

Here is the camera shot, with visible light filter.

Here is the finished mesh. This way is a bit more time consuming, but i still managed to do it in about 5 minutes. (most of that time i was looking for my marker :-) Since the marks were a bit hard to see i had to do some back and forth with the mesh visibility and took me a bit longer to get the vertices matched up, but wasn't too bad.
Currently this calibration requires that your setup have a monitor that is not your projector or it gets a bit more difficult (it is possible, you just do the manual paper-marker route, then switch to the camera view, the downside being that you have to work through the sheets of paper laying on top of your surface which would be a bit of a pain. I am going to add a 'camera snapshot' ability so that you can project the mesh on the surface, take a snapshot, then do the camera mesh. That way you could do it much easier with just your projector as a monitor.
In any case, tomorrow is all about getting the calibration views working in the right order, cleaning up the code and doing some full blown tests and hopefully posting some code for all you to try out (tho it might be Wednesday, but I am optimistic :-)
Cheers!
-b