With the mods you're planning, add in a jet kit sooner rather than later. Ivan's is the best - the slightly vibey nature of the engine at low rpms will be gone, and the throttle response will be very crisp - a lovely improvement to the bike.
Most performance reviews I've seen of the ZX-9R say the 2002-2003 header design is excellent, and there's little need for anything other than a slip-on to see noticeable performance gains. Ivan's plus a Yosh RS-3 slip-on netted me 9.5 horsepower on top, +4-5 throughout the rev-range. That said, if you spend the time on a dyno, I'm sure you can get a full exhaust to help you a bit more than that.
Though Muzzy is a Kawasaki tuner, a used system from them is best avoided, in my opinion. Those I've seen have needed some bending mods to fit well, are very loud, and have very thin wall piping. The thin walls are great for weight reduction, bad for a robusticity. One friend had to just replace his cannister after setting his bike down on it in a parking incident (< 2mph), as both the lower and upper seams on the cannister broke on his Muzzy. I don't think that should happen. He replaced it with an M4, and was happier than with the Muzzy.
If the Hindle has low miles, that is a good choice.