Cerin, i actually didn't go back and look at the code again so take this with a grain of salt, but im pretty sure it will not correctly calculate acceleration (gyro will probably be ok) offsets if the orientation is changed. The program is expecting to see the force of gravity on one axis, and accounts for this when calculating the offsets. If you do not edit the code to change what axis is expecting to see gravity, the offsets probably wont converge, and if they do will be very wrong.
It might be possible to re-write the program to intelligently detect which axis is detecting gravity (reads ~16000 at level rest) and run a smarter calibration routine.
When i needed to reorient my sensors i just fooled the code into switching my axis for me, something like:
axisX = -readAxis(y);
if you go this route you will need to think carefully about how to switch up your axes to maintain a valid coordinate system.