A Mikuni should work with the stock exhaust or a header, either way you may need to rejet the carburetor for optimal performance. The Mikuni may not add peak power by itself but should improve throttle response because the throttle cable is connected directly to the slide, meaning the governor needs to be removed; it isn't plug-n-play. If I were buying a Chikuni/Mikuni kit, which I've been considering, I'd probably buy NR Racing's kit and modify the manifold, or make my own, to avoid having the air filter sticking out from the side of the bike. NR Racing just because I like NR Racing for engine related parts, the header I got from there was impressive, it matched the D-shaped Predator exhaust port in that the hole in the flange was D-shaped
and the tubing was D-shaped where welded to the flange then transitioned to round, unlike many headers with a round hole.
http://www.nrracing.com/product-p/mikuni-22mm-kit-gx200.htm
Other choices
http://www.nrracing.com/category-s/2724.htm