how about this for an idea (it is more hardware based but might still work):
NOTE: this is all theory as i have not tested it yet. i am just putting the idea out there
take a mini mouse like the ones people use for their laptop while travelling take out the board(s) and insert them into a largish marker case. you would need to remove the LED that is used for tracking replace it with an IR LED and move it to the tip. with a little further modification you can have all of your standard mouse buttons (Left, Right, and Middle Wheel) all at your finger tips on the pen. this way the plug and play drivers for most all mice and even the specific drivers for the mouse you use can control Left Click, Right Click, and even Scroll Wheel. From here all that is needed is a modification of atomriot's program that only moves the cursor.
as i have not tested this yet i do not know how well this will work and the biggest problem i forsee will come from calibration (although this also stems from the fact that all of what i stated is theory as i have not yet used any of the software yet) because what i have seen so far is that you have to blink the LED ad each of the four points.
Im messing around with this idea now. It seems much more practical because you wouldnt need a wiimote and there would be much less connection compatibility issues. The problem, like you said, is calibration. I messed around with just using a mouse on top of a computer screen. The cursor moves much faster than the mouse, with my settings, but with some tweaking, its easy to get the cursor to move exactly with the mouse. Its easy to draw with and use just like you would use the IR pen/wiimote. Im still trying to take off certain parts of the mouse and fit it into a pen.
All in all, I think this is a much better solution for a projected whiteboard than using a wiimote, but I could be missing something, that seems to happen a lot.