I'm debating about how to master a song where the music totally changes (different instruments etc.) half way through the song.  Should I split the clips and add effects on each clip? Split them as wav files and master them separately then put them back together? Automation?  

This doesn't sound like a mastering job - sounds like you're still at the mixing stage.
 
Yes, automate your tracks to make the transition as seamless as possible, always allowing for artistic variation of course.

I guess my question is should I master a song with let's say Ozone 7 on the entire song where there are significant musical changes in the song or should I apply separate mastering effects to the different parts of the song to make the song uniform?  

I don't think there are any laws about how to do it. Do it both ways and listen to which sounds better to you.
 

Just to expand on what I posted above, IMHO, if you spend some time addressing this at mix level, the less work you'll have to do when it comes to mastering the track. You won't need to be so heavy handed in getting the 2 sections to mesh together properly.
 
Are you working on a 2 channel "pre master" or are you still working with multitracks?