That's a good look blacking out some of the aluminum looking bits. Mine is the red color option which has the silver fenders that seem to blend well with the other aluminum looking bits. However your bike with the dark gray tank and fenders looks awesome with the blacked out pieces. Well done.
A friend of mine owns a powder coating business and he owed me a favor I would highly recommend the muffler end cap. It really made the whole bike look better even before the other parts were painted. And it sounds better too, not a huge difference but definitely noticeable. I found one online for $62. When I change the oil I will get the cover on the other side of the bike painted gloss black. I definitely think black is the way to go, it really looks sharp I don't think the pic does it justice.
I was hoping someone would add more red to it somewhere because Yamaha went subtle with red and depending on who you ask that might be enough or not enough. Once I get my SCR i might consider adding red somewhere to either the front or rear fenders.