from my reading the 50mm headers with 50/54 midpipe and 54mm end cans is the best way to go as the full 54m system adds top end (9.5K rpm+) power at the expense of more usuable bottom end and mid range
also you will prob need to open up the air inlets in the nose fairing as this is a bottleneck. filter choice can make a big diference too.
forget a Power Commander (unless you have a very cheap one sitting round already), get your ecu repmapped by
BSD or
CJS Racing it will cost the same money and be better than a PCIII and dyno time anyway as more factors can be adjusted and at higher resolution than the PCIII