This is my first mono upgrade as a Linux user. As a windows user I found it best to do a clean install of windows since new chip sets came in to play. Should I do a clean install of kubuntu when I get my new mobo?

As a general rule, Linux systems, especially those using only open source drivers should automatically adapt to the changed hardware, with minimal reconfiguration being required.

However, if you are using the proprietary Nvidia or Ati drivers, it would be advisable to either uninstall them before moving the disk to the new machine, or to perform a clean installation.

In any instance, it should be fine to copy over /home to the new system without changes. If you are going to do this, please make sure both systems do not have anyone logged into graphical interfaces, and the user id numbers on both systems match (if using rsync).