BARS ... and Lowering are the first striking things.
Followed by Solo Seat, (passenger removable pillion) and a clean looking Sissy bar..
Then the rest..
I would leave the engine alone aside from the better breathe..
Ofcourse I am assuming you got rid of the pipes as we speak

 

I'd go with the comfort/appearance stuff first. I put on a short dark windshield righta away. The next thing was probably moving the floorboards out. Then I lowered the bike a little. next came the grips. Put on about 10k miles and finally just put on a new set of mufflers. But with the mufflers, now I'm thinking about the performance stuff, most likely a PCIII and air cleaner from Fuel Moto.