Switching MOBOs is very easy and I have done it before.
This may have been more work than I needed to do, but the reason why I did it this way was to insure that I can go back and to move from a USB stick to a CF as my my boot drive.
Steps I did in 8.0.2:
#1 Save your config file
#2 I labeled all my Sata Ports and made sure that I used the same sata ports for each drive that was in my source Mobo and my dest mobo.
#3 I created a FreeNAS system for the new MOBO (Make sure it is the 64bit version).
#4 Very important -- make sure your FreeNas User Account is the same on the Destination System as your source -- importing your config file will have problems.
#5 Remove the drives from the source to the Dest Mobo using the same and import the config file.
FreeNAS is awsome, I have replace drives, upgraded pools and replace MOBOs and I have not had any problems. I cannot compliment it enough.