It sound like you just need to swap position and orientation coordinates. Here are two methods available with the link object to do this and some sample code. There is also some more info on these in the command index in the docs. You will just need to pass in the proper values to both of these methods.
Code:
#Swap y,z coordinates
link.swapPos([1,3,2])
#Negate yaw value
link.swapEuler([-1,2,3])