Congrats man, they're a blast! I have the same machine in red, bought new this April when they put the 2018s on sale. Mine clunked in the rear as well and my dealer ended up swapping my rear shocks with newer style ones from a 2019 Z1000. That got rid of the noise, ALTHOUGH, when I took the shocks off to take them in to swap them, I also removed the sway bar and in the process I think I discovered that the sway bar mount bushings were a bit loose (bolts were tight, but the bar had some play in the rubber bushings that wasn't noticeable while the ends were connected to the a arms), so I kinda wonder if that is part of the clunking I had. I've thought about putting the swaybar back on to try it. Just something for you to check out.
As for the mud getting in, that was a major issue I also had so I made some mudflaps for the front fenders that hang down about 4" below the plastic fenders and that completely eliminated the wet, muddy thighs. I see you're getting doors so probably won't be necessary. I like the openness of these doors, now that the mud stays off me.
Anyways, enjoy it and take care of it, regular maintenance etc, and it'll be a great toy!