You can lessen the bangs from the exhaust by just blocking off the ais ,also remove the cat from the collector box , both easy to do and free, search on here and youtube for how to for both mods.
As for the ecu, you have two routes, one as you say power commander or an ecu remap. Both require dyno time to get a map that suits your bike perfectly. I bought a second hand juicebox ( virtually the same as a pc3) and K and N filter, then got my local dyno place to do a map for me, juicebox and filter cost £75 from ebay and map and dyno time was about £155. Well worth it as I now have 143bhp at back wheel.
I messed about for ages with different fuel maps from dynojet, two brothers and ones from the American FZ1forum, before I bit the bullet and booked some dyno time, some of the other maps made no difference and some made it worse!
If you do go down the power commander route I can give you a copy of my fuel map to try out.