Hello Lance:
You can try loading that configuration file for the debugger by forcing a full path. Go to Project settings -> Debugger -> Target Settings, and in the initialization file box browse for the correct file in your installation. Please check the next image:

The file you are looking for is inside of M56800E Support\initialization. The inconvenient is that if you get back to the other computer, the error will arise again. To avoid that, you can copy the file to your project folder and reference it from there with "{Project}". Something like:

And about your version question, I'm not quite sure but as far as I know the 5.9 is the version of the whole IDE environment (features, look and feel, user interface, etc), while the 8.3 corresponds to the technology specific software version, in this case it is "CodeWarrior for DSCs", while Freescale has for instance "CodeWarrior for MCUs" and "CodeWarrior for Coldfire", among others.
Hope this is useful :smileyhappy:
Regards
/Jorge Gonzalez