Kyle, the side panels that came on your bike ( carbon) don't fit with the single sided exhaust any longer, no chance.
The heat guard you can cut down, best way is with a large sanding wheel or dremmel but be careful and take your time and don't breath in the carbon dust.
What's with the two holes there on your foot peg bracket?
I can't be 100% but I was told by others that Ducati as of a few month now does incl. the carbon fiber side panels ( the once you have now in plastic) with the Termi exhaust system. Don't know if that is a fact but I was told so by others. If you don't like the black plastic then an alternative is to paint them to match the frame, looks actually pretty good.
Enjoy your time in your garage