So far your ideas sound good.  An aftermarket muffler is a good starting point, and as far as flat black goes, this seems to be the new color style and overall it looks good too.  So, go with your gut and if you end up not liking it thats more time to spend and play with your new bike.  Enjoy the mod bug!

If I read you right you are talking about flat black and gloss black?
Check out the San Carlos Indian pottery called black on black. Please understand that his represents Indian patterns, but you can get a feel for how they look together.
Google images will have lots of images of black on black pottery.

Im one of those all or nothing kind of guys so I think you should paint the entire thing black with a flat/gloss combo and just keep a few little bling tings for a pop. It will go good with the exhaust "pop"   HaHaHa I love that lil guy. But really you should do whatever you think you will like and like flcruzr said, if you don't like it you have reason to spend more time playing with your new bike.

I like the muffler, I did'nt think I would but it looks good. Did you scratch your tank up getting rid of that sticker? Would look even better with one of those black cylinders from a newer model.

Hey that does look nice. I painted my motor and it isn't all that hard to do if you pull it out of the frame and mask off real good. Make sure if you do it you clean in between the fins real good after you rough it up or you will get flakes. I used rattle cans of engine paint. Just make sure you follow the curing instructions. It tells you to run it for 20min. and then let it cool, then run it at operating temp for a while... it's all on the can. I think the black would look good on there.